diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000000000000000000000000000000000000..bc3dce34f449b309195823cc9718a085a3108f09 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,32 @@ +# .readthedocs.yaml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the OS, Python version and other tools you might need +build: + os: ubuntu-22.04 + tools: + python: "3.9" + # You can also specify other tool versions: + # nodejs: "19" + # rust: "1.64" + # golang: "1.19" + +# Build documentation in the "docs/" directory with Sphinx +sphinx: + configuration: docs/source/conf.py + +# Optionally build your docs in additional formats such as PDF and ePub +# formats: +# - pdf +# - epub + +# Optional but recommended, declare the Python requirements required +# to build your documentation +# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html +python: + install: + - requirements: docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..483a4e9600bd7a794750dd52ca24503fdf220133 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1 @@ +sphinx_rtd_theme diff --git a/localise/args.py b/localise/args.py index 16235f17cf0246887ee561532e378aeec6f85073..e26533a0febd3491f1ebcfebf0dfff6f72f4c263 100644 --- a/localise/args.py +++ b/localise/args.py @@ -22,21 +22,38 @@ def parse_arguments(): /path/to/subj002 ... ''')) - p.add_argument('--mask', '-m', required=True, type=str, dest='mask', + + p.add_argument('--seed', '-x', required=True, type=str, dest='seed', + help=textwrap.dedent('''\ + The binary seed mask (doesn't need to include the path). + This script assumes that the mask can be found under + the folder of anatomical masks (--mask_dir), + For example, if the subject folder is /path/to/subject001, + then the binary mask(s) should be stored under /path/to/subject001/roi/left + or /path/to/subject001/roi/right, depending on the hemisphere. + ''')) + + p.add_argument('--hemisphere', '-c', required=True, type=str, dest='hemisphere', + help='Hemisphere of the structure to be localised. Can be left or right.') + + p.add_argument('--mask_dir', '-i', required=True, type=str, dest='mask_dir', help=textwrap.dedent('''\ - Path to the binary seed mask, relative to the subject folder. + Path to the folder that contains anatomical masks, + relative to the subject folder. For example, if the subject folder is /path/to/subject001, - and the path to the binary mask is /path/to/subject001/roi/left/tha.nii.gz, - you should feed in --mask=roi/left/tha.nii.gz. + and the path to the folder is /path/to/subject001/roi, + you should feed in --mask_dir=roi. ''')) - p.add_argument('--target_path', '-p', required=False, type=str, dest='target_path', + + p.add_argument('--target_dir', '-p', required=True, type=str, dest='target_dir', help=textwrap.dedent('''\ Path to the folder that contains connectivity features, relative to the subject folder. For example, if the subject folder is /path/to/subject001, - and the path to the folder is /path/to/subject001/stremlines/left/, - you should feed in --data=streamlines/left. + and the path to the folder is /path/to/subject001/stremlines, + you should feed in --target_dir=streamlines. ''')) + p.add_argument('--target_list', '-l', required=False, type=str, dest='target_list', help=textwrap.dedent('''\ A txt file that contains streamline distribution files, @@ -45,25 +62,36 @@ def parse_arguments(): seeds_to_target2.nii.gz ... ''')) + p.add_argument('--data', '-d', required=False, type=str, dest='data', help=textwrap.dedent('''\ - Path to the *.npy file of connectivity features, relative to the subject folder. + The *.npy file of connectivity features (doesn't need to include the path). + This script assumes that the file can be found under the folder + containing connectivity features (--target_dir). For example, if the subject folder is /path/to/subject001, - and the path to the *.npy file is + and the folder of connectivity features is /path/to/subject001/streamlines, + then the file should be stored under /path/to/subject001/streamlines/left/features.npy or + /path/to/subject001/streamlines/right/features.npy, depending on the hemisphere. /path/to/subject001/stremlines/left/features.npy, you should feed in --data=streamlines/left/features.npy. ''')) + p.add_argument('--atlas', '-a', required=False, type=str, dest='atlas', help=textwrap.dedent('''\ - Path to the atlas of the structure to be localised. + Path to the atlas (group-average proability map) of the structure to be localised, relative to the subject folder. For example, if the subject folder is /path/to/subject001, and the path to the atlas file is - /path/to/subject001/roi/left/atlas.nii.gz, - you should feed in --atlas=roi/left/atlas.nii.gz. - This file must be in the same space as the connectivity features. + /path/to/subject001/atlases/atlas_left.nii.gz, + you should feed in --atlas=atlases/atlas_left.nii.gz. + This file must be in the same reference space as the tract-density maps. + This serves as a prior features to contrain predictions to be not too far away from the group-average position. + If you are under the predict mode and you have specified the structure to be localised (--structure, -r), + you can simply set --atlas=default or -a default, and the script will automatically find the atlas for you. ''')) + p.add_argument('--spatial', action='store_true', required=False, help='Use conditional random field (recommended).') + p.add_argument('--verbose', '-v', action='store_true', required=False, help="Increase output verbosity") @@ -78,21 +106,23 @@ def parse_arguments(): help=textwrap.dedent('''\ Data_type (or modality). can be singleshell, resting-state... ''')) + predict_group.add_argument('--out', '-o', required=False, type=str, dest='out', help=textwrap.dedent('''\ Output filename for the localised structure. ''')) - predict_group.add_argument('--model', required=False, type=str, dest='model', + + predict_group.add_argument('--model', '-m', required=False, type=str, dest='model', help='Filename of the pre-trained model.') # training mode args - train_group.add_argument('--label', required=False, type=str, dest='label', + train_group.add_argument('--label', '-b', required=False, type=str, dest='label', help=textwrap.dedent('''\ Path to the training labels of the structure (required for training). For example, if the subject folder is /path/to/subject001, and the path to the atlas file is /path/to/subject001/roi/left/labels.nii.gz, - you should feed in --atlas=roi/left/labels.nii.gz. + you should feed in --label=roi/left/labels.nii.gz. This file must be in the same space as the connectivity features. ''')) train_group.add_argument('--out_model', required=False, type=str, dest='out_model', @@ -116,8 +146,22 @@ def parse_arguments(): if args.train and args.label is None: p.error('Please specify the training labels.') - - if args.data is None and args.target_path is None: - p.error('At least one of --data or --target_path must be provided.') + + if args.train: + if args.atlas == 'default': + p.error('Please specify the atlas (group-average proability map) for training.') + # under training mode, either specify the target list or the presaved data + if args.data is None and args.target_list is None: + p.error('Please specify the connectivity features or the target list for training.') + + if args.predict: + if args.atlas == 'default' and args.structure is None: + p.error('Please specify the atlas (group-average proability map) for prediction.') + + if args.structure is None and args.model is None: + p.error('Please specify the structure to be localised or the pre-trained model for prediction.') + + if args.model is None and args.data_type is None: + p.error('When using the default model, you must specify the data_type.') return args \ No newline at end of file diff --git a/localise/crf.py b/localise/crf.py deleted file mode 100644 index b913b01bbfb00b67eaa4355627d5f460961435a1..0000000000000000000000000000000000000000 --- a/localise/crf.py +++ /dev/null @@ -1,232 +0,0 @@ -import numpy as np - -import torch -import torch.nn as nn -import torch.nn.functional as F - -class CRF(nn.Module): - def __init__(self, n_spatial_dims, filter_size=3, n_iter=5, requires_grad=True, - returns='logits', smoothness_weight=1, smoothness_theta=1): - super().__init__() - self.n_spatial_dims = n_spatial_dims - self.n_iter = n_iter - self.filter_size = np.broadcast_to(filter_size, n_spatial_dims) - self.returns = returns - self.requires_grad = requires_grad - self._set_param('smoothness_weight', smoothness_weight) - - def _set_param(self, name, init_value): - setattr(self, name, nn.Parameter(torch.tensor(init_value, dtype=torch.float, requires_grad=self.requires_grad))) - - def forward(self, x, spatial_spacings=None): - """ - Propagates the input through the model. - - This function is the forward pass of the model. It takes the input tensor, applies the - Conditional Random Field (CRF) process including initialisation, message passing, - penalizing incompatibility, and adding unary potentials. It finally returns the output - based on the value of the attribute `returns`. - - Parameters - ---------- - x : torch.Tensor - Input tensor of shape ``(batch_size, n_classes, *spatial)``. - spatial_spacings : torch.Tensor, optional - Tensor indicating the spacing between each dimension in the spatial dimensions. - If not provided, it is assumed to be a tensor of ones. - - Returns - ------- - output : torch.Tensor - Output tensor after the CRF process. Its type depends on the value of the attribute `returns`. - If `returns` is 'logits', it returns the logit values. - If `returns` is 'proba', it returns probabilities after applying the softmax function. - If `returns` is 'log-proba', it returns log probabilities. - - Raises - ------ - ValueError - If the spatial dimensions of the input data and model do not match or - if the attribute `returns` is not one of 'logits', 'proba', or 'log-proba'. - """ - batch_size, n_classes, *spatial = x.shape - if len(spatial) != self.n_spatial_dims: - raise ValueError("Spatial dimensions of the data and model do not match.") - - if n_classes == 1: - x = torch.cat([x, torch.zeros(x.shape).to(x)], dim=1) - - if spatial_spacings is None: - spatial_spacings = torch.ones((batch_size, self.n_spatial_dims)) - - negative_unary = x.clone() - - for i in range(self.n_iter): - # initialisation - x = F.softmax(x, dim=1) - - # message passing - x = self.smoothness_weight * self._smoothing_filter(x, spatial_spacings) - - # penalise incompatibility - x = self._compatibility_transform(x) - - # add back unary potentials - x = negative_unary - x - - if self.returns == 'logits': - output = x - elif self.returns == 'proba': - output = F.softmax(x, dim=1) - elif self.returns == 'log-proba': - output = F.log_softmax(x, dim=1) - else: - raise ValueError("Attribute ``returns`` must be 'logits', 'proba' or 'log-proba'.") - - if n_classes == 1: - output = output[:, 0] - output[:, 1] if self.returns == 'logits' else output[:, 0] - output.unsqueeze_(1) - - return output - - def _smoothing_filter(self, x, spatial_spacings): - """ - Parameters - ---------- - x : torch.tensor - Tensor of shape ``(batch_size, n_classes, *spatial)`` with negative unary potentials, e.g. logits. - spatial_spacings : torch.tensor or None - Tensor of shape ``(batch_size, len(spatial))`` with spatial spacings of tensors in batch ``x``. - Returns - ------- - output : torch.tensor - Tensor of shape ``(batch_size, n_classes, *spatial)``. - """ - return torch.stack([self._single_smoothing_filter(x[i], spatial_spacings[i]) for i in range(x.shape[0])]) - - @staticmethod - def _pad(x, filter_size): - """ - Pads the input tensor along all dimensions using the given filter sizes. - - This function calculates the padding for each dimension of the tensor - as half of the corresponding filter size (rounded down, if necessary). - It then applies symmetric padding to the tensor along all dimensions. - - Parameters - ---------- - x : torch.Tensor - The input tensor to be padded. Can have any number of dimensions. - filter_size : list of int - The filter sizes for each dimension of the tensor. The length of this - list should match the number of dimensions in `x`. - - Returns - ------- - torch.Tensor - The input tensor `x`, padded along all dimensions according to the - provided filter sizes. - - """ - padding = [] - for fs in filter_size: - padding += 2 * [fs // 2] - - return F.pad(x, list(reversed(padding))) - - def _single_smooth_filter(self, x): - """ - Applies a single smoothing filter on the input tensor along each dimension. - - This function pads the input tensor, performs a 1-D convolution along each - dimension using a filter of ones, and then reshapes the tensor to its original - shape. This operation can be interpreted as applying a smoothing filter to the - tensor along each dimension independently. - - Parameters - ---------- - x : torch.Tensor - Input tensor of shape ``(n, *spatial)``, where ``n`` is the number of - instances and ``*spatial`` is the spatial dimensions. - - Returns - ------- - torch.Tensor - Output tensor of the same shape as `x`, i.e., ``(n, *spatial)``, after - applying the smoothing filter along each dimension. - - Notes - ----- - The operation is performed independently along each spatial dimension - of the tensor, not in a multivariate sense. - """ - x = self._pad(x, self.filter_size) - for dim in range(1, x.ndim): - x = x.transpose(dim, -1) - shape_before = x.shape[:-1] - x = x.flatten(0, -2).unsqueeze(1) - - # equal weights in the filter - kernel = torch.ones(self.filter_size, ).view(1, 1, -1).to(x) - x = F.conv1d(x, kernel) - - # reshape - x = x.squeeze(1).view(*shape_before, x.shape[-1]).transpose(-1, dim) - - return x - - def _compatibility_transform(self, x): - """ - Applies a compatibility transform on the input tensor. - - This function creates a compatibility matrix by comparing every pair of labels - in the input tensor. Then it performs an Einstein summation between the input tensor - and the compatibility matrix to generate the transformed tensor. - - Parameters - ---------- - x : torch.Tensor - Input tensor of shape ``(batch_size, n_classes, *spatial)``. - - Returns - ------- - output : torch.Tensor - Transformed tensor of shape ``(batch_size, n_classes, *spatial)``. - - Notes - ----- - This function is generally used in the context of Conditional Random Field (CRF) models - to model the compatibility (or incompatibility) between different labels. - """ - labels = torch.arange(x.shape[1]) - compatibility_matrix = self._compatibility_function(labels, labels.unsqueeze(1)).to(x) - # dot product across the n_class dimension - return torch.einsum('ij..., jk -> ik...', x, compatibility_matrix) - - @staticmethod - def _compatibility_function(label1, label2): - """ - Computes the compatibility between two input tensors. - - This function returns a tensor with the same shape as the inputs containing - the compatibility score between each pair of corresponding labels in the input tensors. - The compatibility is computed as the negative of the equality comparison - between the input labels, cast to float. - - Parameters - ---------- - label1 : torch.Tensor - Input tensor containing label values. - label2 : torch.Tensor - Input tensor containing label values. Must be broadcastable to `label1`. - - Returns - ------- - compatibility : torch.Tensor - Tensor containing compatibility scores, with the same shape as the inputs. - - Notes - ----- - The input tensors must be broadcastable to each other. - """ - return -(label1 == label2).float() \ No newline at end of file diff --git a/localise/modes.py b/localise/modes.py new file mode 100644 index 0000000000000000000000000000000000000000..01613e4590d1d9ad760247e372e5f606bada7aa2 --- /dev/null +++ b/localise/modes.py @@ -0,0 +1,174 @@ +import os, logging +from pathlib import Path +from localise.load import load_data, load_features, ShuffledDataLoader +from localise.train import train_without_val +from localise.predict import apply_pretrained_model +from localise.utils import save_nifti + + +PKG_PATH = Path(__file__).parent.parent + +def get_subjects(subject_path): + """Load subjects from file or directory.""" + if os.path.isfile(subject_path): + with open(subject_path, 'r') as f: + return [line.strip() for line in f] + elif os.path.isdir(subject_path): + return [subject_path] + else: + raise ValueError(f'Invalid subject path: {subject_path}. Please specify a correct subject dir or txt file.') + +def return_hemisphere(hemisphere): + ## a function to check hemisphere + if isinstance(hemisphere, str): + if hemisphere.lower() in ['left', 'l']: + hemisphere = 'left' + elif hemisphere.lower() in ['right', 'r']: + hemisphere = 'right' + else: + raise ValueError(f'Invalid hemisphere: {hemisphere}. Please specify left or right.') + else: + raise ValueError(f'Invalid hemisphere: {hemisphere}. Please specify left or right.') + + return hemisphere + +def check_params(mask, mask_dir, target_dir, data, hemisphere): + # create mask name + if mask_dir is None: + raise ValueError('Please specify the directory for anatomical masks (relative to the subject folder).') + + mask = os.path.join(mask_dir, hemisphere, mask) + + # create target_path + if target_dir is None: + raise ValueError('Please specify the directory for target masks (relative to the subject folder).') + + target_path = os.path.join(target_dir, hemisphere) + + if data is not None: + data = os.path.join(target_dir, hemisphere, data) + + return mask, mask_dir, target_path, data + +def predict_mode(subject, mask, mask_dir=None, structure=None, target_dir=None, target_list=None, + data=None, atlas=None, out=None, model=None, spatial=True, + data_type=None, hemisphere=None, verbose=True): + + if verbose: + logging.basicConfig(level=logging.INFO) + + logging.info('Predict mode on.\n') + subjects = get_subjects(subject) + hemisphere = return_hemisphere(hemisphere) + mask, mask_dir, target_path, data = check_params(mask, mask_dir, target_dir, data, hemisphere) + + # create output name + if out is None: + raise ValueError('Please specify the output name.') + + if atlas == 'default': + if structure is None: + raise ValueError('Please specify the structure (--structure, -s) if using the default atlases.') + # create default atlas path + atlas = os.path.join(mask_dir, hemisphere, f'{structure}.nii.gz') + + if model is None: + # error checking + if structure is None: + raise ValueError('When using the default model, you must specify the structure.') + if data_type is None: + raise ValueError('When using the default model, you must specify the data_type.') + + logging.info(f'Using the default model for {structure} on {data_type}.') + + # load the default model. + model_dir = os.path.join(PKG_PATH, 'resources', 'models', structure, data_type, hemisphere) + model_name = 'spatial_model' if spatial else 'model' + model_name = f'{model_name}_with_prior.pth' if atlas is not None else f'{model_name}.pth' + model = os.path.join(model_dir, model_name) + + if not os.path.exists(model): + raise ValueError(f'We dont have a pretrained model for {structure} {data_type}.') + + target_list_fname = os.path.join(PKG_PATH, 'resources', 'data', + f'{structure}_default_target_list.txt') + # checking whether or not to use default + if data is None and target_list is None: + # load default target list + logging.info('Using default target list.') + + with open(target_list_fname, 'r') as f: + target_list = [line.strip() for line in f] + + else: + logging.info(f'Please make sure your data or target_list matches the order of the default target list {target_list_fname}.') + + else: + logging.info(f'Using the model stored in {model}.') + + # check errors. either specify --data, or specify both --target_path and --target_list + if data is None: + if target_path is None: + raise ValueError("Please specify --target_path if you didn't specify --data") + if target_list is None: + raise ValueError("Please specify --target_list if you didn't specify --data when you are not using the default model.") + + data = [ + load_features( + subject=subject, + mask_name=mask, + target_path=target_path, + target_list=target_list, + data=data, + atlas=atlas, + power=[2, 1, 0.5] + ) + for subject in subjects + ] + + predictions = apply_pretrained_model(data, model, spatial_model=spatial) + + logging.info('Localise done. Now saving results...') + # save to nii files + for subject, prediction in zip(subjects, predictions): + save_nifti(prediction.detach().numpy()[:, -1], os.path.join(subject, mask), os.path.join(subject, out)) + + logging.info('Done.') + + return predictions + + +def train_mode(subject, mask, label, mask_dir=None, target_dir=None, + target_list=None, data=None, atlas=None, out_model=None, + spatial=True, hemisphere=None, epochs=100, verbose=True): + + if verbose: + logging.basicConfig(level=logging.INFO) + + logging.info('Training mode on.\n') + subjects = get_subjects(subject) + hemisphere = return_hemisphere(hemisphere) + mask, mask_dir, target_path, data = check_params(mask, mask_dir, target_dir, data, hemisphere) + + if data is None and target_list is None: + raise ValueError("Please specify --target_list if you didn't specify --data.") + + data = [ + load_data( + subject=subject, + mask_name=mask, + label_name=label, + target_path=target_path, + target_list=target_list, + data=data, + atlas=atlas + ) + for subject in subjects + ] + + dataloader = ShuffledDataLoader(data) + model = train_without_val(dataloader, n_epochs=epochs, + spatial_model=spatial, + model_save_path=out_model) + + return model \ No newline at end of file diff --git a/localise/predict.py b/localise/predict.py index e59227935148e65daed730fb4eae89bccce7b714..bbbcfeeaff67e8741f1b10ac3474a9ee145ef410 100644 --- a/localise/predict.py +++ b/localise/predict.py @@ -35,7 +35,7 @@ def apply_pretrained_model(data, model_save_path, model="Linear", spatial_model= n_kernels=n_kernels, is_crf=spatial_model) # Load the saved model parameters - m.load_state_dict(torch.load(model_save_path)) + m.load_state_dict(torch.load(model_save_path), strict=False) # Ensure model is in evaluation mode m.eval() diff --git a/localise/utils.py b/localise/utils.py index c40b0fa10ee3bd563016441e879faeed5b7cbdb7..ce60e87bc987487e3febf6f5f74fbcc2a8ce5088 100644 --- a/localise/utils.py +++ b/localise/utils.py @@ -1,11 +1,7 @@ -import os, logging, subprocess +import subprocess import numpy as np import nibabel as nib -import subprocess from pathlib import Path -from localise.load import load_data, load_features, ShuffledDataLoader -from localise.train import train, train_with_val, train_without_val -from localise.predict import apply_pretrained_model PKG_PATH = Path(__file__).parent.parent @@ -88,232 +84,6 @@ def save_nifti_4D(data, mask_file, output_file): # Save the NIfTI image nib.save(output_nifti, output_file) - -def get_subjects(subject_path): - """Load subjects from file or directory.""" - if os.path.isfile(subject_path): - with open(subject_path, 'r') as f: - return [line.strip() for line in f] - elif os.path.isdir(subject_path): - return [subject_path] - else: - raise ValueError(f'Invalid subject path: {subject_path}. Please specify a correct subject dir or txt file.') - - -def predict_mode(subject, mask, structure=None, target_path=None, target_list=None, - data=None, atlas=None, out=None, model=None, spatial=True, data_type=None): - - logging.info('Predict mode on.\n') - subjects = get_subjects(subject) - - if model is None: - # error checking - if structure is None: - raise ValueError('When using the default model, you must specify the structure.') - if data_type is None: - raise ValueError('When using the default model, you must specify the data_type.') - - logging.info(f'Using the default model for {structure} on {data_type}.') - # load the default model. - model_dir = os.path.join(PKG_PATH, 'resources', 'models', structure, data_type) - model_name = f'{structure}_spatial_model.pth' if spatial else f'{structure}_model.pth' - model = os.path.join(model_dir, model_name) - - if not os.path.exists(model): - raise ValueError(f'We dont have a pretrained model for {structure} {data_type}.') - - target_list_fname = os.path.join(PKG_PATH, 'resources', 'data', - f'{structure}_default_target_list.txt') - # checking whether or not to use default - if data is None and target_list is None: - # load default target list - logging.info('Using default target list.') - - with open(target_list_fname, 'r') as f: - target_list = [line.strip() for line in f] - - else: - logging.info(f'Please make sure your data or target_list matches the order of the default target list {target_list_fname}.') - - else: - logging.info(f'Using the model stored in {model}.') - - # check errors. either specify --data, or specify both --target_path and --target_list - if data is None: - if target_path is None: - raise ValueError("Please specify --target_path if you didn't specify --data") - if target_list is None: - raise ValueError("Please specify --target_list if you didn't specify --data when you are not using the default model.") - - # load connectivity features - data = [ - load_features( - subject=subject, - mask_name=mask, - target_path=target_path, - target_list=target_list, - data=data, - atlas=atlas - ) - for subject in subjects - ] - - predictions = apply_pretrained_model(data, model, spatial_model=spatial) - - # save to nii files - for subject, prediction in zip(subjects, predictions): - save_nifti(prediction.detach().numpy()[:, -1], os.path.join(subject, mask), os.path.join(subject, out)) - - return predictions - - -def train_mode(subject, mask, label, target_path=None, - target_list=None, data=None, atlas=None, out_model=None, - spatial=True, epochs=100): - - logging.info('Training mode on.\n') - subjects = get_subjects(subject) - - if data is None and target_list is None: - raise ValueError("Please specify --target_list if you didn't specify --data.") - - if data is None and target_path is None: - raise ValueError("Please specify --target_path if you didn't specify --data.") - - data = [ - load_data( - subject=subject, - mask_name=mask, - label_name=label, - target_path=target_path, - target_list=target_list, - data=data, - atlas=atlas - ) - for subject in subjects - ] - - dataloader = ShuffledDataLoader(data) - model = train_without_val(dataloader, n_epochs=epochs, - spatial_model=spatial, - model_save_path=out_model) - - return model - - -def create_masks(ref, warp, out=None, aparc=None, brainmask=None): - """ - Create masks based on provided parameters. - - Parameters: - - ref (str): Reference string. - - warp (str): Warp string. - - out (Optional[str]): Output string. Defaults to None. - - aparc (Optional[str]): Aparc string. Defaults to None. - - brainmask (Optional[str]): Brainmask string. Defaults to None. - - Raises: - - ValueError: If required environment variables or files are missing. - """ - if "FSLDIR" not in os.environ: - raise ValueError("FSLDIR environment variable does not exist.") - if not os.path.isfile(ref): - raise ValueError(f"{ref} does not exist.") - if not os.path.isfile(warp): - raise ValueError(f"{warp} does not exist.") - - cmd = os.path.join(PKG_PATH, "scripts", "create_masks") - args = [cmd, f"--ref={ref}", f"--warp={warp}"] - - params = [("out", out), ("aparc", aparc), ("brainmask", brainmask)] - for param, value in params: - if value is not None: - args.append(f"--{param}={value}") - - run_command(args) - - -def create_tracts(samples_dir, input_dir, seed=None, xfm=None, ref=None, - out=None, brainmask=None, nsteps=None, cthr=None, - fibthresh=None, nsamples=None, steplength=None, - sampvox=None, distthresh=None, gpu=True): - """ - Create tracts based on provided parameters. - - Parameters are described in the function signature. - - Raises: - - ValueError: If required environment variables or directories are missing. - """ - - if "FSLDIR" not in os.environ: - raise ValueError("FSLDIR environment variable is missing.") - if not os.path.isdir(samples_dir): - raise ValueError(f"Directory '{samples_dir}' is missing.") - if not os.path.isdir(input_dir): - raise ValueError(f"Directory '{input_dir}' is missing.") - - cmd = os.path.join(PKG_PATH, "scripts", "create_tracts") - args = [cmd, f"--samples={samples_dir}", f"--inputdir={input_dir}"] - - params = [ - ("out", out), - ("seed", seed), - ("xfm", xfm), - ("ref", ref), - ("brainmask", brainmask), - ("nsteps", nsteps), - ("cthr", cthr), - ("fibthresh", fibthresh), - ("nsamples", nsamples), - ("steplength", steplength), - ("sampvox", sampvox), - ("distthresh", distthresh) - ] - for param, value in params: - if value is not None: - args.append(f"--{param}={value}") - - if gpu: - args.append("--gpu") - - run_command(args) - - -def connectivity_driven(target1, target2, out, target3=None, - thr1=None, thr2=None, thr3=None, thr=None): - """ - Perform a connectivity-driven analysis using two or three target images. - - Parameters are described in the function signature. - - Raises: - - ValueError: If required environment variables or directories are missing. - """ - if "FSLDIR" not in os.environ: - raise ValueError("FSLDIR environment variable is missing.") - if not os.path.isfile(target1): - raise ValueError(f"{target1} does not exist.") - if not os.path.isfile(target2): - raise ValueError(f"{target2} does not exist.") - - cmd = os.path.join(PKG_PATH, "scripts", "connectivity_driven") - args = [cmd, f"--target1={target1}", f"--target2={target2}", f"--out={out}"] - - params = [ - ("thr1", thr1), - ("thr2", thr2), - ("thr3", thr3), - ("target3", target3), - ("thr", thr) - ] - for param, value in params: - if value is not None: - args.append(f"--{param}={value}") - - run_command(args) - - def run_command(cmd): try: subprocess.run(cmd, check=True) diff --git a/resources/data/vim_default_target_list.txt b/resources/data/vim_default_target_list.txt index 575f2054219dcd350f2ad6d8602ccccf35ca767e..b8678207f5c0cb9a3c971921b7025332e9802340 100644 --- a/resources/data/vim_default_target_list.txt +++ b/resources/data/vim_default_target_list.txt @@ -73,41 +73,88 @@ seeds_to_11172.nii.gz seeds_to_11173.nii.gz seeds_to_11174.nii.gz seeds_to_11175.nii.gz -seeds_to_to_precentral1.nii.gz -seeds_to_to_precentral2.nii.gz -seeds_to_to_precentral3.nii.gz -seeds_to_to_precentral4.nii.gz -seeds_to_to_precentral5.nii.gz -seeds_to_to_postcentral1.nii.gz -seeds_to_to_postcentral2.nii.gz -seeds_to_to_postcentral3.nii.gz -seeds_to_to_postcentral4.nii.gz -seeds_to_to_postcentral5.nii.gz -seeds_to_ar1.nii.gz -seeds_to_ar2.nii.gz -seeds_to_ar3.nii.gz -seeds_to_ar4.nii.gz -seeds_to_ar5.nii.gz -seeds_to_or1.nii.gz -seeds_to_or2.nii.gz -seeds_to_or3.nii.gz -seeds_to_or4.nii.gz -seeds_to_or5.nii.gz -seeds_to_or6.nii.gz -seeds_to_str1.nii.gz -seeds_to_str2.nii.gz -seeds_to_str3.nii.gz -seeds_to_str4.nii.gz -seeds_to_str5.nii.gz -seeds_to_str6.nii.gz -seeds_to_atr1.nii.gz -seeds_to_atr2.nii.gz -seeds_to_atr3.nii.gz -seeds_to_atr4.nii.gz -seeds_to_atr5.nii.gz -seeds_to_atr6.nii.gz -seeds_to_scpct1.nii.gz -seeds_to_scpct2.nii.gz -seeds_to_scpct3.nii.gz -seeds_to_SCPCT_brainstem_60.nii.gz -seeds_to_contra_cerebellum_wm.nii.gz +seeds_to_ar_mask1.nii.gz +seeds_to_ar_mask2.nii.gz +seeds_to_ar_mask3.nii.gz +seeds_to_ar_mask4.nii.gz +seeds_to_ar_mask5.nii.gz +seeds_to_ar_mask6.nii.gz +seeds_to_ar_mask7.nii.gz +seeds_to_ar_mask8.nii.gz +seeds_to_or_mask1.nii.gz +seeds_to_or_mask2.nii.gz +seeds_to_or_mask3.nii.gz +seeds_to_or_mask4.nii.gz +seeds_to_or_mask5.nii.gz +seeds_to_or_mask6.nii.gz +seeds_to_or_mask7.nii.gz +seeds_to_or_mask8.nii.gz +seeds_to_or_mask9.nii.gz +seeds_to_or_mask10.nii.gz +seeds_to_str_mask1.nii.gz +seeds_to_str_mask2.nii.gz +seeds_to_str_mask3.nii.gz +seeds_to_str_mask4.nii.gz +seeds_to_str_mask5.nii.gz +seeds_to_str_mask6.nii.gz +seeds_to_str_mask7.nii.gz +seeds_to_str_mask8.nii.gz +seeds_to_str_mask9.nii.gz +seeds_to_str_mask10.nii.gz +seeds_to_atr_mask1.nii.gz +seeds_to_atr_mask2.nii.gz +seeds_to_atr_mask3.nii.gz +seeds_to_atr_mask4.nii.gz +seeds_to_atr_mask5.nii.gz +seeds_to_atr_mask6.nii.gz +seeds_to_atr_mask7.nii.gz +seeds_to_atr_mask8.nii.gz +seeds_to_fx_mask1.nii.gz +seeds_to_fx_mask2.nii.gz +seeds_to_fx_mask3.nii.gz +seeds_to_fx_mask4.nii.gz +seeds_to_fx_mask5.nii.gz +seeds_to_fx_mask6.nii.gz +seeds_to_fx_mask7.nii.gz +seeds_to_fx_mask8.nii.gz +seeds_to_fx_mask9.nii.gz +seeds_to_fx_mask10.nii.gz +seeds_to_to_precentral_mask1.nii.gz +seeds_to_to_precentral_mask2.nii.gz +seeds_to_to_precentral_mask3.nii.gz +seeds_to_to_precentral_mask4.nii.gz +seeds_to_to_precentral_mask5.nii.gz +seeds_to_to_precentral_mask6.nii.gz +seeds_to_to_precentral_mask7.nii.gz +seeds_to_to_precentral_mask8.nii.gz +seeds_to_to_precentral_mask9.nii.gz +seeds_to_to_precentral_mask10.nii.gz +seeds_to_to_precentral_mask11.nii.gz +seeds_to_to_precentral_mask12.nii.gz +seeds_to_to_postcentral_mask1.nii.gz +seeds_to_to_postcentral_mask2.nii.gz +seeds_to_to_postcentral_mask3.nii.gz +seeds_to_to_postcentral_mask4.nii.gz +seeds_to_to_postcentral_mask5.nii.gz +seeds_to_to_postcentral_mask6.nii.gz +seeds_to_to_postcentral_mask7.nii.gz +seeds_to_to_postcentral_mask8.nii.gz +seeds_to_to_postcentral_mask9.nii.gz +seeds_to_to_postcentral_mask10.nii.gz +seeds_to_to_postcentral_mask11.nii.gz +seeds_to_to_postcentral_mask12.nii.gz +seeds_to_scpct_mask1.nii.gz +seeds_to_scpct_mask2.nii.gz +seeds_to_scpct_mask3.nii.gz +seeds_to_scpct_mask4.nii.gz +seeds_to_scpct_mask5.nii.gz +seeds_to_scpct_mask6.nii.gz +seeds_to_scpct_mask7.nii.gz +seeds_to_scpct_mask8.nii.gz +seeds_to_scpct_mask9.nii.gz +seeds_to_scpct_mask10.nii.gz +seeds_to_scpct_mask11.nii.gz +seeds_to_scpct_mask12.nii.gz +seeds_to_scpct_mask13.nii.gz +seeds_to_scpct_mask14.nii.gz +seeds_to_scpct_mask15.nii.gz diff --git a/resources/models/vim/2mm/left/model.pth 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b/scripts/connectivity_driven index 1c5d34cc1ab110aede8a5e92c172b3dcb829572e..8880eb86b96c84a67931f0134f73e8b62f74d0f1 100755 --- a/scripts/connectivity_driven +++ b/scripts/connectivity_driven @@ -2,7 +2,7 @@ Usage() { echo "" - echo "Usage: ./connectivity_driven.sh --target1=m1.nii.gz --target2=cerebellum.nii.gz" + echo "Usage: connectivity_driven --target1=m1.nii.gz --target2=cerebellum.nii.gz" echo "" echo "creates anatomical masks in reference space (--ref) for tractography and stores them in the output dir (--out)" echo "if the cortical parcellation file (--aparc) not provided, uses standard masks instead" diff --git a/scripts/create_masks b/scripts/create_masks index 2c36a885276611be62423bf202a2d645009b8266..b3e30c67cad72e5cb1ce71896143a0e6b50fae0a 100755 --- a/scripts/create_masks +++ b/scripts/create_masks @@ -2,24 +2,27 @@ Usage() { echo "" - echo "Usage: ./create_masks.sh --ref=t1.nii.gz --warp=standard2str.nii.gz --out=outputdir --aparc=aparc.a2009s+aseg.nii.gz" + echo "Usage: create_masks --ref=subj001/t1.nii.gz --warp=subj001/standard2str.nii.gz --out=subj001/roi --aparc=subj001/aparc.a2009s+aseg.nii.gz" + echo " or with short flags:" + echo " create_masks -r subj001/t1.nii.gz -w subj001/standard2str.nii.gz -o subj001/roi -a subj001/aparc.a2009s+aseg.nii.gz" echo "" - echo "creates anatomical masks in reference space (--ref) for tractography and stores them in the output dir (--out)" - echo "if the cortical parcellation file (--aparc) not provided, uses standard masks instead" - echo "" - echo "<options>:" - echo "--ref (the reference image, usually in the individual T1 native space)" - echo "--warp (the warp field that maps the MNI standard space to individual T1 space)" - echo "--aparc (the cortical segmentation file from Freesurfer, either in *.mgz or *.nii.gz/*.nii)" - echo "--out (optional, the output directory to store the anatomical masks. if not provided, create a folder called roi in the same directory as the reference image)" - echo "--brainmask (optional, the binary brain mask in the reference space)" - echo "--queue (optional, the queue jobs should be submitted to. Run locally if not specified.)" - echo "--njobs (optional, the number of jobs to run in parallel locally.)" + echo "Description:" + echo " Creates anatomical masks in reference space (--ref) for tractography and stores them in the output directory (--out)." echo "" + echo "Options:" + echo " -r, --ref The reference image, typically in the individual T1 native space." + echo " -w, --warp The warp field mapping the MNI standard space to individual T1 space." + echo " -a, --aparc Cortical segmentation file from Freesurfer (in *.mgz, *.nii.gz, or *.nii formats)." + echo " -o, --out (Optional) Directory to store the anatomical masks." + echo " Defaults to a 'roi' folder in the same directory as the reference image." + echo " -b, --brainmask (Optional) Binary brain mask in the reference space." + echo " -q, --queue (Optional) Queue for job submissions. Defaults to local execution." + echo " -n, --njobs (Optional) Number of jobs to run in parallel locally. Defaults to 1." echo "" exit 1 } + [ "$1" = "" ] && Usage if [ -z "$FSLDIR" ]; then @@ -56,41 +59,76 @@ njobs=1 for arg in "$@" do case $arg in - --help) + -h|--help) Usage ;; + -r|--ref) + shift + ref="$1" + shift + ;; + -o|--out) + shift + out="$1" + shift + ;; + -w|--warp) + shift + warp="$1" + shift + ;; + -a|--aparc) + shift + aparc="$1" + shift + ;; + -b|--brainmask) + shift + brainmask="$1" + shift + ;; + -q|--queue) + shift + queue="$1" + shift + ;; + -n|--njobs) + shift + njobs="$1" + shift + ;; --ref=*) - ref="${arg#*=}" - shift - ;; + ref="${arg#*=}" + shift + ;; --out=*) - out="${arg#*=}" - shift - ;; + out="${arg#*=}" + shift + ;; --warp=*) - warp="${arg#*=}" - shift - ;; + warp="${arg#*=}" + shift + ;; --aparc=*) - aparc="${arg#*=}" - shift - ;; + aparc="${arg#*=}" + shift + ;; --brainmask=*) - brainmask="${arg#*=}" - shift - ;; + brainmask="${arg#*=}" + shift + ;; --queue=*) - queue="${arg#*=}" - shift - ;; + queue="${arg#*=}" + shift + ;; --njobs=*) - njobs="${arg#*=}" - shift - ;; + njobs="${arg#*=}" + shift + ;; *) - echo "Unknown option: $arg" - Usage - exit 1 + # echo "Error: Invalid argument: $arg" + # Usage + # exit 1 ;; esac done @@ -178,14 +216,14 @@ if [ ! -z "$aparc" ]; then kk=`expr $k - 11100` echo "$FSLDIR/bin/fslmaths $aparc -thr $k -uthr $k -bin $out/left/$kk" >> $out/create_masks_cmds done - echo "$FSLDIR/bin/fslmaths $aparc -thr 11100 -uthr 12175 -bin $out/left/cortex" >> $out/create_masks_cmds + #echo "$FSLDIR/bin/fslmaths $aparc -thr 11100 -uthr 12175 -bin $out/cortex" >> $out/create_masks_cmds ### right hemisphere cortical masks echo "echo Create right hemisphere cortical ROIs based on the provided $aparc file..." >> $out/create_masks_cmds for k in {12101..12175}; do kk=`expr $k - 12100` echo "$FSLDIR/bin/fslmaths $aparc -thr $k -uthr $k -bin $out/right/$kk" >> $out/create_masks_cmds done - echo "$FSLDIR/bin/fslmaths $aparc -thr 11100 -uthr 12175 -bin $out/right/cortex" >> $out/create_masks_cmds + echo "$FSLDIR/bin/fslmaths $aparc -thr 11100 -uthr 12175 -bin $out/cortex" >> $out/create_masks_cmds fi #$FSLDIR/bin/fslmaths $out/right/cortex -add $out/left/cortex -bin $out/cortex @@ -277,7 +315,10 @@ if [ -z "$queue" ]; then fi bash "$out/create_masks_scpct_cmds" else - fsl_sub -q $queue -N create_masks -l $out -t "$out/create_masks_cmds" - fsl_sub -q $queue -N create_masks_scpct -l $out "$out/create_masks_scpct_cmds" - echo "jobs submitted." + if [ ! -d $out/log ]; then + mkdir $out/logs + fi; + fsl_sub -q $queue -N create_masks -l $out/logs -t "$out/create_masks_cmds" + fsl_sub -q $queue -N create_masks_scpct -l $out/logs "bash $out/create_masks_scpct_cmds" + echo "jobs submitted. Logs will be stored under $out/logs." fi diff --git a/scripts/create_tracts b/scripts/create_tracts index 873a496da6e1f8f120a278fe13d8318111826992..9de74d4fd90f8323a5fd9a31be91e0df40262982 100755 --- a/scripts/create_tracts +++ b/scripts/create_tracts @@ -2,32 +2,35 @@ Usage() { echo "" - echo "Usage: ./create_tracts.sh --inputdir=/path/to/roi_folder --samples=/path/to/data.bedpostX --seed=/path/to/seed.nii.gz" + echo "Usage: create_tracts -i subj001/roi -m subj001/dMRI.bedpostX -s seed.nii.gz" echo "" echo "creates tracts for the specified seed, using fiber samples estimated via BedpostX" - echo "if seed is not specified, use tha.nii.gz as default seed under the input ROI folder." echo "" echo "<options>:" - echo "--samples BedpostX directory that stores fibre orientation files, e.g., data.bedpostX" - echo "--inputdir Input directory that stores left and right hemisphere anatomical masks in native T1 space" - #echo "--hemi Left or right hemisphere" - echo "--seed Optional, the seed mask, usually in the individual T1 native space - default is tha.nii.gz under inputdir" - echo "--xfm Optional, the transformation matrix that maps the reference T1 space to the diffusion space" - echo "--ref Optional, the reference image, usually in the individual T1 native space" - echo "--out Optional, the output directory to store tract density maps - default is inputdir/hemi/streamlines" - echo "--brainmask Optional, the binary brain mask in the reference space)" - echo "--nsteps Optional, number of steps per sample - default=2000" - echo "--cthr Optional, curvature threshold - default=0.2" - echo "--fibthresh Optional, volume fraction before subsidary fibre orientations are considered - default=0.01" - echo "--nsamples Optional, number of samples - default=10000" - echo "--steplength Optional, steplength in mm - default=0.5" - echo "--sampvox Optional, sample random points within a sphere with radius x mm from the center of the seed voxels" - echo "--distthresh Optional, discards samples shorter than this threshold (in mm - default=0)" - echo "--gpu Optional, use the gpu version of probtractx2" - echo "--queue Optional, the queue jobs should be submitted to. Run locally if not specified." + echo "-m, --samples BedpostX directory storing fibre orientation files. Example: data.bedpostX" + echo "-i, --inputdir Input directory storing left and right hemisphere anatomical masks in native T1 space" + echo "-s, --seed Seed mask, usually in the individual T1 native space (path not needed if in the inputdir)." + echo "-o, --out Output directory for tract density maps. Defaults to 'tracts_out' in the inputdir." + echo "-x, --xfm (Optional) Transformation matrix mapping the reference T1 space to the diffusion space. " + echo " Necessary if diffusion is not aligned to the reference T1 space." + echo "-r, --ref (Optional) Reference image, usually in the individual T1 native space." + echo " Necessary if xfm (-x) is specified." + echo "-b, --brainmask (Optional) Binary brain mask in the diffusion space." + echo "-n, --nsteps (Optional) Number of steps per sample. Default=2000" + echo "-c, --cthr (Optional) Curvature threshold. Default=0.2" + echo "-f, --fibthresh (Optional) Volume fraction threshold before considering subsidiary fibre orientations. Default=0.01" + echo "-j, --nsamples (Optional) Number of samples. Default=10000" + echo "-l, --steplength (Optional) Steplength in mm. Default=0.5" + echo "-p, --sampvox (Optional) Sample random points within a sphere of radius 'x' mm from the seed voxel center." + echo "-d, --distthresh (Optional) Discards samples shorter than this threshold (in mm). Default=0" + echo "-g, --gpu (Optional) Use the GPU version of probtractx2." + echo "-q, --queue (Optional) The job queue to submit to. Runs locally if unspecified." + echo "" + echo "For more detailed information, consult the documentation." exit 1 } + [ "$1" = "" ] && Usage for arg in "$@" @@ -69,11 +72,12 @@ fibthresh=0.01 sampvox=1.0 distthresh=0 prog="probtrackx2" + ### parse arguments for arg in "$@" do case $arg in - --help) + -h|--help) Usage ;; --seed=*) @@ -136,7 +140,7 @@ do distthresh="${arg#*=}" shift ;; - --gpu) + -g|--gpu) prog="probtrackx2_gpu" shift ;; @@ -144,10 +148,90 @@ do queue="${arg#*=}" shift ;; + -s|--seed) + seed=$2 + shift + shift + ;; + -r|--ref) + ref=$2 + shift + shift + ;; + -m|--samples) + samples=$2 + shift + shift + ;; + -o|--out) + out=$2 + shift + shift + ;; + -i|--inputdir) + inputdir=$2 + shift + shift + ;; + -b|--brainmask) + brainmask=$2 + shift + shift + ;; + -x|--xfm) + xfm=$2 + shift + shift + ;; + -n|--nsteps) + nsteps=$2 + shift + shift + ;; + -c|--cthr) + cthr=$2 + shift + shift + ;; + -v|--verbose) + verbose=$2 + shift + shift + ;; + -l|--steplength) + steplength=$2 + shift + shift + ;; + -j|--nsamples) + nsamples=$2 + shift + shift + ;; + -f|--fibthresh) + fibthresh=$2 + shift + shift + ;; + -p|--sampvox) + sampvox=$2 + shift + shift + ;; + -d|--distthresh) + distthresh=$2 + shift + shift + ;; + -q|--queue) + queue=$2 + shift + shift + ;; *) - echo "Unknown option: $arg" - Usage - exit 1 + # echo "Unknown option: $arg" + # Usage + # exit 1 ;; esac done @@ -184,19 +268,17 @@ if [ ! -z "$queue" ]; then fi if [ -z "$out" ]; then - out=$refpath/streamlines + out=$($dirname "$refpath")/streamlines echo "output directory not specified. create $out to store tract density maps in reference space" fi if [ -z "$seed" ]; then - echo "Seed mask not specified. default using $inputdir/tha.nii.gz..." - seed=$inputdir/tha - if [ ! -f $seed.nii.gz ] && [ ! -f $seed.nii ]; then - echo "$seed not found." - exit 1 - fi + echo "Error: Missing required argument --seed, the seed mask for tractography." + exit 1 fi +seed=$(basename $seed) + if [ -z "$brainmask" ]; then brainmask=$samples/nodif_brain_mask if [ ! -f $brainmask.nii.gz ] && [ ! -f $brainmask.nii ]; then @@ -210,51 +292,65 @@ if [ ! -d $out ]; then mkdir -p $out fi -## create a list containing the anatomical masks -echo $inputdir/ar_mask{1..8}.nii.gz > $inputdir/targets.txt; -echo $inputdir/or_mask{1..10}.nii.gz >> $inputdir/targets.txt; -echo $inputdir/str_mask{1..10}.nii.gz >> $inputdir/targets.txt; -echo $inputdir/atr_mask{1..8}.nii.gz >> $inputdir/targets.txt; -echo $inputdir/fx_mask{1..10}.nii.gz >> $inputdir/targets.txt; -echo $inputdir/to_precentral_mask{1..12}.nii.gz >> $inputdir/targets.txt; -echo $inputdir/to_postcentral_mask{1..12}.nii.gz >> $inputdir/targets.txt; -echo $inputdir/{1..75}.nii.gz >> $inputdir/targets.txt; +if [ -f $out/create_tracts_cmds ]; then + rm $out/create_tracts_cmds +fi +# for left and right hemispheres +for hemi in left right; do + if [ ! -d $out/$hemi ]; then + mkdir $out/$hemi + fi + ## create a list containing the anatomical masks + echo $inputdir/$hemi/ar_mask{1..8}.nii.gz > $inputdir/$hemi/targets.txt; + echo $inputdir/$hemi/or_mask{1..10}.nii.gz >> $inputdir/$hemi/targets.txt; + echo $inputdir/$hemi/str_mask{1..10}.nii.gz >> $inputdir/$hemi/targets.txt; + echo $inputdir/$hemi/atr_mask{1..8}.nii.gz >> $inputdir/$hemi/targets.txt; + echo $inputdir/$hemi/fx_mask{1..10}.nii.gz >> $inputdir/$hemi/targets.txt; + echo $inputdir/$hemi/to_precentral_mask{1..12}.nii.gz >> $inputdir/$hemi/targets.txt; + echo $inputdir/$hemi/to_postcentral_mask{1..12}.nii.gz >> $inputdir/$hemi/targets.txt; + echo $inputdir/$hemi/{1..75}.nii.gz >> $inputdir/$hemi/targets.txt; -opts="-x $seed -s $samples/merged -m $brainmask --dir=$out" -opts="$opts --verbose=$verbose --cthr=$cthr --nsteps=$nsteps --steplength=$steplength --nsamples=$nsamples --fibthresh=$fibthresh" -opts="$opts --distthresh=$distthresh --sampvox=$sampvox -l --onewaycondition --forcedir --pd --opd --os2t --modeuler" + opts="-x $inputdir/$hemi/$seed -s $samples/merged -m $brainmask --dir=$out/$hemi" + opts="$opts --verbose=$verbose --cthr=$cthr --nsteps=$nsteps --steplength=$steplength --nsamples=$nsamples --fibthresh=$fibthresh" + opts="$opts --distthresh=$distthresh --sampvox=$sampvox -l --onewaycondition --forcedir --pd --opd --os2t --modeuler" -if [ ! -z "$xfm" ]; then - opts="$opts --xfm=$xfm" - if [ ! -z "$ref" ]; then - opts="$opts --seedref=$ref" - else - opts="$opts --seedref=$seed" + if [ ! -z "$xfm" ]; then + opts="$opts --xfm=$xfm" + if [ ! -z "$ref" ]; then + opts="$opts --seedref=$ref" + else + opts="$opts --seedref=$inputdir/$hemi/$seed" + fi fi -fi -cmd="$FSLDIR/bin/$prog $opts" -cmd="$cmd --targetmasks=$inputdir/targets.txt" -cmd="$cmd --avoid=$inputdir/cerebellum --stop=$inputdir/cortex" + cmd="$FSLDIR/bin/$prog $opts" + cmd="$cmd --targetmasks=$inputdir/$hemi/targets.txt" + cmd="$cmd --avoid=$inputdir/$hemi/cerebellum --stop=$inputdir/cortex" -### run tractography... -echo $cmd > $out/create_tracts_cmds; -#eval $cmd; + ### run tractography... + echo $cmd >> $out/create_tracts_cmds; + #eval $cmd; + + echo $inputdir/$hemi/scpct_mask{1..15}.nii.gz > $inputdir/$hemi/scpct_targets.txt; + echo $inputdir/$hemi/cerebellum_target.nii.gz >> $inputdir/$hemi/scpct_targets.txt; + cmd="$FSLDIR/bin/$prog $opts" + cmd="$cmd --targetmasks=$inputdir/$hemi/scpct_targets.txt" + cmd="$cmd --avoid=$inputdir/$hemi/exclusion --stop=$inputdir/$hemi/stop_for_scpct" + echo $cmd >> $out/create_tracts_cmds; + #eval $cmd; +done -echo $inputdir/scpct_mask{1..15}.nii.gz > $inputdir/targets.txt; -echo $inputdir/cerebellum_target.nii.gz >> $inputdir/targets.txt; -cmd="$FSLDIR/bin/$prog $opts" -cmd="$cmd --targetmasks=$inputdir/targets.txt" -cmd="$cmd --avoid=$inputdir/exclusion --stop=$inputdir/stop_for_scpct" -echo $cmd >> $out/create_tracts_cmds; -#eval $cmd; if [ -z "$queue" ]; then bash $out/create_tracts_cmds else - if gpu; then - fsl_sub -q $queue -c cuda -N create_tracts -l $out -t $out/create_tracts_cmds + if [ ! -d $out/log ]; then + mkdir $out/logs + fi; + if $gpu; then + fsl_sub -q $queue -c cuda -N create_tracts -l $out/logs -t $out/create_tracts_cmds else - fsl_sub -q $queue -N create_tracts -l $out -t $out/create_tracts_cmds + fsl_sub -q $queue -N create_tracts -l $out/logs -t $out/create_tracts_cmds fi + echo "jobs submitted. Logs will be stored under $out/logs." fi diff --git a/scripts/localise b/scripts/localise index 15fb3606115d8ab71f1f82bf187f2858db36111e..312c169b90bc11799219ec8821908a8e525f50bc 100755 --- a/scripts/localise +++ b/scripts/localise @@ -1,18 +1,19 @@ #!/usr/bin/env python -from localise.utils import predict_mode, train_mode -from localise.args import parse_arguments +from localise.modes import predict_mode, train_mode +from localise.args import parse_arguments + if __name__ == "__main__": args = parse_arguments() if args.predict: - predict_mode(subject=args.subject, mask=args.mask, structure=args.structure, - target_path=args.target_path, target_list=args.target_list, - data=args.data, atlas=args.atlas, out=args.out, - model=args.model, spatial=args.spatial, data_type=args.data_type) + predict_mode(subject=args.subject, mask=args.seed, mask_dir=args.mask_dir, structure=args.structure, + target_dir=args.target_dir, target_list=args.target_list, data=args.data, atlas=args.atlas, + out=args.out, model=args.model, spatial=args.spatial, data_type=args.data_type, + hemisphere=args.hemisphere, verbose=args.verbose) elif args.train: - train_mode(args.subject, args.mask, args.label, - args.target_path, args.target_list, - args.data, args.atlas, args.out_model, - args.spatial, args.epochs) + train_mode(subject=args.subject, mask=args.seed, label=args.label, mask_dir=args.mask_dir, + target_dir=args.target_dir, target_list=args.target_list, data=args.data, atlas=args.atlas, + out_model=args.out_model, spatial=args.spatial, hemisphere=args.hemisphere, epochs=args.epochs, + verbose=args.verbose) else: raise ValueError("Exactly one of --train or --predict must be specified.") \ No newline at end of file diff --git a/tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz b/tests/test_data/101915/T1w_acpc_dc_restore.nii.gz similarity index 70% rename from tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz rename to tests/test_data/101915/T1w_acpc_dc_restore.nii.gz index 75ca40801587e82c25378fd3a131dbff8227dd94..36d19e22d6c1f42fc0f43d1aea50239e12c04b76 100644 Binary files a/tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz and b/tests/test_data/101915/T1w_acpc_dc_restore.nii.gz differ diff --git a/tests/test_data/101915/aparc.a2009s+aseg.nii.gz b/tests/test_data/101915/aparc.a2009s+aseg.nii.gz new file mode 100755 index 0000000000000000000000000000000000000000..2e5d7b49027e2a40d7c35ba530b39cba2787a612 Binary files /dev/null and b/tests/test_data/101915/aparc.a2009s+aseg.nii.gz differ diff --git a/tests/test_data/101915/roi/aparc.a2009s+aseg.nii.nii.gz b/tests/test_data/101915/roi/aparc.a2009s+aseg.nii.nii.gz new file mode 100644 index 0000000000000000000000000000000000000000..c0c12108d6a84b4872f3edba8f27fbe7ac430536 Binary files /dev/null and b/tests/test_data/101915/roi/aparc.a2009s+aseg.nii.nii.gz differ diff --git a/tests/test_data/101915/roi/brain_mask.nii.gz b/tests/test_data/101915/roi/brain_mask.nii.gz new file mode 100644 index 0000000000000000000000000000000000000000..c6e9b3c2384993ca791326eb937230fd9ee277ef Binary files /dev/null and b/tests/test_data/101915/roi/brain_mask.nii.gz differ diff --git a/tests/test_data/101915/roi/create_masks_cmds b/tests/test_data/101915/roi/create_masks_cmds new file mode 100644 index 0000000000000000000000000000000000000000..bc0d33aa065c380a10be8ad7c88bcf5adb203547 --- /dev/null +++ b/tests/test_data/101915/roi/create_masks_cmds @@ -0,0 +1,338 @@ +echo Create cerebellar ROIs based on the provided 101915/roi/aparc.a2009s+aseg.nii.nii.gz file... +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 6 -uthr 8 -bin 101915/roi/left/cerebellum +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 45 -uthr 47 -bin 101915/roi/right/cerebellum +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 7 -uthr 7 -bin 101915/roi/right/cerebellum_target +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 46 -uthr 46 -bin 101915/roi/left/cerebellum_target +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 24 -uthr 24 -bin 101915/roi/csf +echo Create left hemisphere cortical ROIs based on the provided 101915/roi/aparc.a2009s+aseg.nii.nii.gz file... +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11101 -uthr 11101 -bin 101915/roi/left/1 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11102 -uthr 11102 -bin 101915/roi/left/2 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11103 -uthr 11103 -bin 101915/roi/left/3 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11104 -uthr 11104 -bin 101915/roi/left/4 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11105 -uthr 11105 -bin 101915/roi/left/5 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11106 -uthr 11106 -bin 101915/roi/left/6 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11107 -uthr 11107 -bin 101915/roi/left/7 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11108 -uthr 11108 -bin 101915/roi/left/8 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11109 -uthr 11109 -bin 101915/roi/left/9 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11110 -uthr 11110 -bin 101915/roi/left/10 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11111 -uthr 11111 -bin 101915/roi/left/11 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11112 -uthr 11112 -bin 101915/roi/left/12 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11113 -uthr 11113 -bin 101915/roi/left/13 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11114 -uthr 11114 -bin 101915/roi/left/14 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11115 -uthr 11115 -bin 101915/roi/left/15 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11116 -uthr 11116 -bin 101915/roi/left/16 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11117 -uthr 11117 -bin 101915/roi/left/17 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11118 -uthr 11118 -bin 101915/roi/left/18 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11119 -uthr 11119 -bin 101915/roi/left/19 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11120 -uthr 11120 -bin 101915/roi/left/20 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11121 -uthr 11121 -bin 101915/roi/left/21 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11122 -uthr 11122 -bin 101915/roi/left/22 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11123 -uthr 11123 -bin 101915/roi/left/23 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11124 -uthr 11124 -bin 101915/roi/left/24 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/aparc.a2009s+aseg.nii.nii.gz -thr 11125 -uthr 11125 -bin 101915/roi/left/25 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 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101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/scpct_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/scpct_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/scpct_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/scpct_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask11 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/scpct_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask12 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/scpct_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask13 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/scpct_mask13 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask14 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/scpct_mask14 --interp=nn 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101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/str_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/str_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/str_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/str_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/str_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/str_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/str_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/str_mask10 --interp=nn 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-o 101915/roi/left/atr_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/atr_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/atr_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/atr_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/atr_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/ar_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/ar_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/ar_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/ar_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/ar_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/ar_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/ar_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/ar_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/or_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/fx_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask11 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask12 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_precentral_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask11 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask12 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/to_postcentral_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/tha -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/tha --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/vim -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/vim +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/exclusion -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/exclusion --interp=nn +echo Create masks for right hemisphere... +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask11 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask12 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask13 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask13 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask14 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask14 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask15 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/scpct_mask15 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/str_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/str_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/atr_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/atr_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/atr_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/atr_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/atr_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/atr_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/atr_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/atr_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/atr_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/atr_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/atr_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/atr_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/atr_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/atr_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/atr_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/atr_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/ar_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/ar_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/ar_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/ar_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/ar_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/ar_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/ar_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/ar_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/ar_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/ar_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/ar_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/ar_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/ar_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/ar_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/ar_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/ar_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/or_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/or_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/fx_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask11 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask12 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_precentral_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask1 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask2 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask3 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask4 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask5 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask6 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask7 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask8 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask9 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask10 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask11 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask12 -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/to_postcentral_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/tha -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/tha --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/vim -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/vim +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/exclusion -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/exclusion --interp=nn diff --git a/tests/test_data/101915/roi/create_masks_scpct_cmds b/tests/test_data/101915/roi/create_masks_scpct_cmds new file mode 100644 index 0000000000000000000000000000000000000000..d14860a639aa57cef20578fff29a73a5e9f8a8a8 --- /dev/null +++ b/tests/test_data/101915/roi/create_masks_scpct_cmds @@ -0,0 +1,8 @@ +echo Create SCPCT-related ROIs... +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win/software/packages/fsl/6.0.6/data/standard/MNI152_T1_1mm_brain_mask -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/brain_mask --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/SCPCT -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/left/SCPCT +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/left/SCPCT -thr 0.0001 -bin 101915/roi/left/SCPCT_bin +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/brain_mask -rem 101915/roi/left/SCPCT_bin -bin -rem 101915/roi/left/tha -bin 101915/roi/left/stop_for_scpct +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 101915/T1w_acpc_dc_restore.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/SCPCT -w 101915/standard1_to_native1.25_warp.nii.gz -o 101915/roi/right/SCPCT +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/right/SCPCT -thr 0.0001 -bin 101915/roi/right/SCPCT_bin +/well/win/software/packages/fsl/6.0.6/bin/fslmaths 101915/roi/brain_mask -rem 101915/roi/right/SCPCT_bin -bin -rem 101915/roi/right/tha -bin 101915/roi/right/stop_for_scpct diff --git a/tests/test_data/101915/roi/csf.nii.gz b/tests/test_data/101915/roi/csf.nii.gz new file mode 100644 index 0000000000000000000000000000000000000000..957c323c4e601d0b077858890b87cb1ebe4eba53 Binary files /dev/null and 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0000000000000000000000000000000000000000..de51dea840130c00a181a2339321fbb7c124c8fe --- /dev/null +++ b/tests/test_data/104416/roi/create_masks_cmds @@ -0,0 +1,338 @@ +echo Create cerebellar ROIs based on the provided tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz file... +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 6 -uthr 8 -bin tests/test_data/104416/roi/left/cerebellum +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 45 -uthr 47 -bin tests/test_data/104416/roi/right/cerebellum +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 7 -uthr 7 -bin tests/test_data/104416/roi/right/cerebellum_target +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 46 -uthr 46 -bin tests/test_data/104416/roi/left/cerebellum_target +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 24 -uthr 24 -bin tests/test_data/104416/roi/csf +echo Create left hemisphere cortical ROIs based on the provided tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz file... +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11101 -uthr 11101 -bin tests/test_data/104416/roi/left/1 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11102 -uthr 11102 -bin tests/test_data/104416/roi/left/2 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11103 -uthr 11103 -bin tests/test_data/104416/roi/left/3 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11104 -uthr 11104 -bin tests/test_data/104416/roi/left/4 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11105 -uthr 11105 -bin tests/test_data/104416/roi/left/5 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11106 -uthr 11106 -bin tests/test_data/104416/roi/left/6 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11107 -uthr 11107 -bin tests/test_data/104416/roi/left/7 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11108 -uthr 11108 -bin tests/test_data/104416/roi/left/8 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11109 -uthr 11109 -bin tests/test_data/104416/roi/left/9 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11110 -uthr 11110 -bin tests/test_data/104416/roi/left/10 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11111 -uthr 11111 -bin tests/test_data/104416/roi/left/11 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11112 -uthr 11112 -bin tests/test_data/104416/roi/left/12 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11113 -uthr 11113 -bin tests/test_data/104416/roi/left/13 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11114 -uthr 11114 -bin tests/test_data/104416/roi/left/14 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11115 -uthr 11115 -bin tests/test_data/104416/roi/left/15 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11116 -uthr 11116 -bin tests/test_data/104416/roi/left/16 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11117 -uthr 11117 -bin tests/test_data/104416/roi/left/17 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11118 -uthr 11118 -bin tests/test_data/104416/roi/left/18 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11119 -uthr 11119 -bin tests/test_data/104416/roi/left/19 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11120 -uthr 11120 -bin tests/test_data/104416/roi/left/20 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11121 -uthr 11121 -bin tests/test_data/104416/roi/left/21 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11122 -uthr 11122 -bin tests/test_data/104416/roi/left/22 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11123 -uthr 11123 -bin tests/test_data/104416/roi/left/23 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11124 -uthr 11124 -bin tests/test_data/104416/roi/left/24 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11125 -uthr 11125 -bin tests/test_data/104416/roi/left/25 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11126 -uthr 11126 -bin tests/test_data/104416/roi/left/26 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11127 -uthr 11127 -bin tests/test_data/104416/roi/left/27 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11128 -uthr 11128 -bin tests/test_data/104416/roi/left/28 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11129 -uthr 11129 -bin tests/test_data/104416/roi/left/29 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11130 -uthr 11130 -bin tests/test_data/104416/roi/left/30 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11131 -uthr 11131 -bin tests/test_data/104416/roi/left/31 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11132 -uthr 11132 -bin tests/test_data/104416/roi/left/32 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11133 -uthr 11133 -bin tests/test_data/104416/roi/left/33 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11134 -uthr 11134 -bin tests/test_data/104416/roi/left/34 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11135 -uthr 11135 -bin tests/test_data/104416/roi/left/35 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11136 -uthr 11136 -bin tests/test_data/104416/roi/left/36 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11137 -uthr 11137 -bin tests/test_data/104416/roi/left/37 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11138 -uthr 11138 -bin tests/test_data/104416/roi/left/38 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11139 -uthr 11139 -bin tests/test_data/104416/roi/left/39 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11140 -uthr 11140 -bin tests/test_data/104416/roi/left/40 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11141 -uthr 11141 -bin tests/test_data/104416/roi/left/41 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11142 -uthr 11142 -bin tests/test_data/104416/roi/left/42 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11143 -uthr 11143 -bin tests/test_data/104416/roi/left/43 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11144 -uthr 11144 -bin tests/test_data/104416/roi/left/44 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11145 -uthr 11145 -bin tests/test_data/104416/roi/left/45 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11146 -uthr 11146 -bin tests/test_data/104416/roi/left/46 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11147 -uthr 11147 -bin tests/test_data/104416/roi/left/47 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11148 -uthr 11148 -bin tests/test_data/104416/roi/left/48 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11149 -uthr 11149 -bin tests/test_data/104416/roi/left/49 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11150 -uthr 11150 -bin tests/test_data/104416/roi/left/50 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11151 -uthr 11151 -bin tests/test_data/104416/roi/left/51 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11152 -uthr 11152 -bin tests/test_data/104416/roi/left/52 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11153 -uthr 11153 -bin tests/test_data/104416/roi/left/53 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11154 -uthr 11154 -bin tests/test_data/104416/roi/left/54 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11155 -uthr 11155 -bin tests/test_data/104416/roi/left/55 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11156 -uthr 11156 -bin tests/test_data/104416/roi/left/56 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11157 -uthr 11157 -bin tests/test_data/104416/roi/left/57 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11158 -uthr 11158 -bin tests/test_data/104416/roi/left/58 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11159 -uthr 11159 -bin tests/test_data/104416/roi/left/59 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11160 -uthr 11160 -bin tests/test_data/104416/roi/left/60 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11161 -uthr 11161 -bin tests/test_data/104416/roi/left/61 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11162 -uthr 11162 -bin tests/test_data/104416/roi/left/62 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11163 -uthr 11163 -bin tests/test_data/104416/roi/left/63 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11164 -uthr 11164 -bin tests/test_data/104416/roi/left/64 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11165 -uthr 11165 -bin tests/test_data/104416/roi/left/65 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11166 -uthr 11166 -bin tests/test_data/104416/roi/left/66 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11167 -uthr 11167 -bin tests/test_data/104416/roi/left/67 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11168 -uthr 11168 -bin tests/test_data/104416/roi/left/68 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11169 -uthr 11169 -bin tests/test_data/104416/roi/left/69 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11170 -uthr 11170 -bin tests/test_data/104416/roi/left/70 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11171 -uthr 11171 -bin tests/test_data/104416/roi/left/71 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11172 -uthr 11172 -bin tests/test_data/104416/roi/left/72 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11173 -uthr 11173 -bin tests/test_data/104416/roi/left/73 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11174 -uthr 11174 -bin tests/test_data/104416/roi/left/74 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11175 -uthr 11175 -bin tests/test_data/104416/roi/left/75 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11100 -uthr 12175 -bin tests/test_data/104416/roi/left/cortex +echo Create right hemisphere cortical ROIs based on the provided tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz file... +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 12101 -uthr 12101 -bin tests/test_data/104416/roi/right/1 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 12102 -uthr 12102 -bin tests/test_data/104416/roi/right/2 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 12103 -uthr 12103 -bin tests/test_data/104416/roi/right/3 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 12104 -uthr 12104 -bin 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12174 -bin tests/test_data/104416/roi/right/74 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 12175 -uthr 12175 -bin tests/test_data/104416/roi/right/75 +/well/win/software/packages/fsl/6.0.6/bin/fslmaths tests/test_data/104416/roi/aparc.a2009s+aseg.nii.gz -thr 11100 -uthr 12175 -bin tests/test_data/104416/roi/right/cortex +echo Create masks for left hemisphere... +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask9 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask11 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask12 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask13 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask13 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask14 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask14 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/scpct_mask15 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/scpct_mask15 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask9 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/str_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/str_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/atr_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/atr_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/atr_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/atr_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/atr_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/atr_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/atr_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/atr_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/atr_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/ar_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/ar_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/ar_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/ar_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/ar_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/ar_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/ar_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/ar_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/ar_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask9 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/or_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/or_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask9 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/fx_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/fx_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask9 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask11 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_precentral_mask12 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_precentral_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask9 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask11 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/to_postcentral_mask12 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/to_postcentral_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/tha -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/tha --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/vim -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/vim +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/left/exclusion -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/left/exclusion --interp=nn +echo Create masks for right hemisphere... +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask9 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask11 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/scpct_mask12 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/scpct_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i 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/well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/fx_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/fx_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_precentral_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_precentral_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i 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/well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask6 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_precentral_mask6 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask7 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_precentral_mask7 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask8 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_precentral_mask8 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask9 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_precentral_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_precentral_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask11 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_precentral_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_precentral_mask12 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_precentral_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask1 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_postcentral_mask1 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask2 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_postcentral_mask2 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask3 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_postcentral_mask3 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask4 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_postcentral_mask4 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask5 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_postcentral_mask5 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i 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/well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask9 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_postcentral_mask9 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask10 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_postcentral_mask10 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask11 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_postcentral_mask11 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/to_postcentral_mask12 -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/to_postcentral_mask12 --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/tha -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/tha --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/vim -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/vim +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win-biobank/users/gbb787/python-localise/resources/MNI_roi/right/exclusion -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/right/exclusion --interp=nn diff --git a/tests/test_data/104416/roi/create_masks_scpct_cmds b/tests/test_data/104416/roi/create_masks_scpct_cmds new file mode 100644 index 0000000000000000000000000000000000000000..4bd068dedfb56af34c37e88815ebc3a7d56c2fea --- /dev/null +++ b/tests/test_data/104416/roi/create_masks_scpct_cmds @@ -0,0 +1,9 @@ +echo Create SCPCT-related ROIs... +echo brainmask not provided. use standard brain mask MNI152_T1_1mm_brain_mask instead... +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r tests/test_data/104416/T1w_acpc_dc_restore_1.nii.gz -i /well/win/software/packages/fsl/6.0.6/data/standard/MNI152_T1_1mm_brain_mask -w tests/test_data/104416/standard1_to_native0.7_warp.nii.gz -o tests/test_data/104416/roi/brain_mask --interp=nn +/well/win/software/packages/fsl/6.0.6/bin/applywarp -r 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+seeds_to_scpct_mask13.nii.gz +seeds_to_scpct_mask14.nii.gz +seeds_to_scpct_mask15.nii.gz diff --git a/tests/test_modes.py b/tests/test_modes.py new file mode 100644 index 0000000000000000000000000000000000000000..4f781f9694d4fbb75906ef7508b4ddc1bd6951f6 --- /dev/null +++ b/tests/test_modes.py @@ -0,0 +1,132 @@ +import os, pytest +from localise.modes import get_subjects +from localise.modes import predict_mode, train_mode +from localise.modes import return_hemisphere, check_params +from pathlib import Path +from unittest.mock import patch + + +path_to_data = Path(__file__).parent / 'test_data' + +def test_get_subjects(tmp_path): + # Test with file + d = tmp_path / "subdir" + d.mkdir() + p = d / "subjects.txt" + p.write_text("subject1\nsubject2\n") + + result = get_subjects(str(p)) + assert result == ["subject1", "subject2"] + + # Test with directory + result = get_subjects(str(d)) + assert result == [str(d)] + + # Test with invalid path + with pytest.raises(ValueError): + get_subjects(str(tmp_path / "nonexistent")) + +def test_return_hemisphere(): + # Test valid inputs for left hemisphere + assert return_hemisphere('left') == 'left' + assert return_hemisphere('l') == 'left' + assert return_hemisphere('L') == 'left' + + # Test valid inputs for right hemisphere + assert return_hemisphere('right') == 'right' + assert return_hemisphere('r') == 'right' + assert return_hemisphere('R') == 'right' + + # Test invalid input + with pytest.raises(ValueError, match=r"Invalid hemisphere: center. Please specify left or right."): + return_hemisphere('center') + + # Test empty input + with pytest.raises(ValueError, match=r"Invalid hemisphere: . Please specify left or right."): + return_hemisphere('') + +def test_check_params(): + mask_dir = "masks" + target_dir = "targets" + hemisphere = "left" + + # Test valid inputs + mask, m_dir, target_path, data = check_params("mask1.nii.gz", mask_dir, target_dir, "data1.nii.gz", hemisphere) + assert mask == os.path.join(mask_dir, hemisphere, "mask1.nii.gz") + assert m_dir == mask_dir + assert target_path == os.path.join(target_dir, hemisphere) + assert data == os.path.join(target_dir, hemisphere, "data1.nii.gz") + + # Test missing mask_dir + with pytest.raises(ValueError, match="Please specify the directory for anatomical masks"): + check_params("mask1.nii.gz", None, target_dir, "data1.nii.gz", hemisphere) + + # Test missing target_dir + with pytest.raises(ValueError, match="Please specify the directory for target masks"): + check_params("mask1.nii.gz", mask_dir, None, "data1.nii.gz", hemisphere) + + # Test None data + mask, m_dir, target_path, data = check_params("mask1.nii.gz", mask_dir, target_dir, None, hemisphere) + assert data is None + +def test_predict_mode(): + subject = f'{path_to_data}/101915' + mask = 'mist_left_thalamus_mask_small_1.nii.gz' + mask_dir = 'roi' + hemisphere = 'left' + target_dir = 'streamlines' + target_list = f'{path_to_data}/models/vim_default_target_list160.txt' + atlas = 'roi/left/vim.nii.gz' + out = 'roi/left/prediction.nii.gz' + model = f'{path_to_data}/models/tmp_model160_2mm_single32.pth' + + predict_mode(subject=subject, mask=mask, mask_dir=mask_dir, target_dir=target_dir, + target_list=target_list, atlas=atlas, out=out, model=model, hemisphere=hemisphere) + assert os.path.isfile(os.path.join(subject, out)) + os.remove(os.path.join(subject, out)) + + predict_mode(subject=subject, mask=mask, mask_dir=mask_dir, structure='vim', target_dir=target_dir, + atlas='default', out=out, data_type='2mm_single32', hemisphere=hemisphere) + assert os.path.isfile(os.path.join(subject, out)) + os.remove(os.path.join(subject, out)) + + with pytest.raises(ValueError): + predict_mode(subject=subject, mask=mask, mask_dir=mask_dir, target_dir=target_dir, + atlas=atlas, out=out, hemisphere=hemisphere) + + with pytest.raises(ValueError): + predict_mode(subject=subject, mask=mask, mask_dir=mask_dir, structure='vim', target_dir=target_dir, + atlas=atlas, out=out, hemisphere=hemisphere) + + with pytest.raises(ValueError): + predict_mode(subject=subject, mask=mask, mask_dir=mask_dir, structure='vim', target_dir=target_dir, + atlas=atlas, out=out, hemisphere=None) + + predict_mode(subject=subject, mask=mask, mask_dir=mask_dir, structure='vim', target_dir=target_dir, + target_list=target_list, atlas=atlas, out=out, data_type='2mm_single32', hemisphere=hemisphere) + + assert os.path.isfile(os.path.join(subject, out)) + os.remove(os.path.join(subject, out)) + + predict_mode(subject=subject, mask=mask, mask_dir=mask_dir, target_dir=target_dir, + data='X160_small_1mm.npy', structure='vim', spatial=False, + atlas=None, out=out, data_type='2mm_single32', hemisphere=hemisphere) + + assert os.path.isfile(os.path.join(subject, out)) + os.remove(os.path.join(subject, out)) + +def test_train_mode(): + subject = f'{path_to_data}/100206' + mask_dir = 'roi' + mask = 'tha_small.nii.gz' + label = 'high-quality-labels/left/labels.nii.gz' + target_dir = 'streamlines' + target_list = f'{path_to_data}/models/targets_list113_left.txt' + atlas = 'roi/left/atlas.nii.gz' + out_model = f'{path_to_data}/models/test_model.pth' + + train_mode(subject=subject, mask=mask, label=label, mask_dir=mask_dir, target_dir=target_dir, + target_list=target_list, atlas=atlas, out_model=out_model, hemisphere='left') + + assert os.path.isfile(out_model) + os.remove(out_model) diff --git a/tests/test_scripts.py b/tests/test_scripts.py index beea4cf53f78d6a317bd1e4d6e7995a79ce5f972..b211683160a1f4b42c2ac0afa81964349798a7c6 100644 --- a/tests/test_scripts.py +++ b/tests/test_scripts.py @@ -1,7 +1,7 @@ import pytest from unittest.mock import patch from localise.args import parse_arguments -from localise.utils import create_masks, create_tracts, connectivity_driven + def test_parse_arguments(): @@ -9,34 +9,90 @@ def test_parse_arguments(): with patch('argparse._sys.argv', ['localise', '--train', '--subject', '/path/to/subject', - '--mask', 'roi/mask', - '--label', 'roi/label', + '--seed', 'seed.nii.gz', + '--mask_dir', 'roi', + '--label', 'roi/label/label.nii.gz', '--out_model', 'model', - '--target_path', 'data/left', + '--target_dir', 'tracts', + '--hemisphere', 'left', + '--data', 'data.npy', '--epochs', '100']): args = parse_arguments() assert args.train assert args.subject == '/path/to/subject' - assert args.mask == 'roi/mask' - assert args.label == 'roi/label' + assert args.seed == 'seed.nii.gz' + assert args.mask_dir == 'roi' + assert args.label == 'roi/label/label.nii.gz' assert args.out_model == 'model' + assert args.target_dir == 'tracts' + assert args.data == 'data.npy' assert args.epochs == 100 # Testing the prediction mode with patch('argparse._sys.argv', ['localise', '--predict', '--subject', '/path/to/subject', - '--mask', 'roi/mask', - '--data', 'data/data', + '--seed', 'seed.nii.gz', + '--mask_dir', 'roi', + '--target_dir', 'tracts', + '--data', 'data.npy', + '--hemisphere', 'right', + '--structure', 'vim', + '--data_type', 'single32', '--out', 'output']): args = parse_arguments() assert args.predict assert args.subject == '/path/to/subject' - assert args.mask == 'roi/mask' - assert args.data == 'data/data' + assert args.mask_dir == 'roi' + assert args.data == 'data.npy' assert args.out == 'output' + assert args.seed == 'seed.nii.gz' + assert args.target_dir == 'tracts' + assert args.structure == 'vim' + + # Testing the prediction mode with structure and model missing + with pytest.raises(SystemExit): + with patch('argparse._sys.argv', + ['localise', '--predict', + '--subject', '/path/to/subject', + '--seed', 'seed.nii.gz', + '--mask_dir', 'roi', + '--target_dir', 'tracts', + '--data', 'data.npy', + '--hemisphere', 'right', + '--out', 'output']): + args = parse_arguments() + + # Testing the prediction mode with default atlas + with pytest.raises(SystemExit): + with patch('argparse._sys.argv', + ['localise', '--predict', + '--subject', '/path/to/subject', + '--seed', 'seed.nii.gz', + '--mask_dir', 'roi', + '--target_dir', 'tracts', + '--data', 'data.npy', + '--hemisphere', 'right', + '--model', 'model.pth', + '--atlas', 'default', + '--out', 'output']): + args = parse_arguments() + + # Testing the prediction mode with default atlas + with patch('argparse._sys.argv', + ['localise', '--predict', + '--subject', '/path/to/subject', + '--seed', 'seed.nii.gz', + '--mask_dir', 'roi', + '--target_dir', 'tracts', + '--data', 'data.npy', + '--hemisphere', 'right', + '--structure', 'vim', + '--out', 'output']): + with pytest.raises(SystemExit): + args = parse_arguments() # Test the missing argument in training mode with pytest.raises(SystemExit): @@ -57,94 +113,3 @@ def test_parse_arguments(): with pytest.raises(SystemExit): with patch('argparse._sys.argv', ['localise']): args = parse_arguments() - - -def test_create_masks(): - # Mocking the environment variable - with patch.dict('os.environ', {'FSLDIR': 'some_value'}): - # Mocking the os.path.isfile function to always return True - with patch('os.path.isfile', return_value=True): - # Mocking the subprocess.run function to do nothing - with patch('subprocess.run') as mock_subprocess: - ref = "some_ref_path" - warp = "some_warp_path" - create_masks(ref, warp) - mock_subprocess.assert_called_once() - - # Testing for missing FSLDIR environment variable - with patch.dict('os.environ', {}, clear=True): - with pytest.raises(ValueError, match="FSLDIR environment variable does not exist."): - create_masks("some_ref_path", "some_warp_path") - - # Testing for missing ref file - with patch.dict('os.environ', {'FSLDIR': 'some_value'}): - with patch('os.path.isfile', side_effect=[False, True]): - with pytest.raises(ValueError, match=f"{ref} does not exist."): - create_masks(ref, warp) - - # Testing for missing warp file - with patch.dict('os.environ', {'FSLDIR': 'some_value'}): - with patch('os.path.isfile', side_effect=[True, False]): - with pytest.raises(ValueError, match=f"{warp} does not exist."): - create_masks(ref, warp) - - -def test_create_tracts(): - # Mocking the environment variable - with patch.dict('os.environ', {'FSLDIR': 'some_value'}): - # Mocking the os.path.isdir function to always return True - with patch('os.path.isdir', return_value=True): - # Mocking the subprocess.run function to do nothing - with patch('subprocess.run') as mock_subprocess: - samples_dir = "some_samples_dir_path" - input_dir = "some_input_dir_path" - create_tracts(samples_dir, input_dir) - mock_subprocess.assert_called_once() - - # Testing for missing FSLDIR environment variable - with patch.dict('os.environ', {}, clear=True): - with pytest.raises(ValueError, match="FSLDIR environment variable is missing."): - create_tracts(samples_dir, input_dir) - - # Testing for missing samples_dir - with patch.dict('os.environ', {'FSLDIR': 'some_value'}): - with patch('os.path.isdir', side_effect=[False, True]): - with pytest.raises(ValueError, match=f"Directory '{samples_dir}' is missing."): - create_tracts(samples_dir, input_dir) - - # Testing for missing input_dir - with patch.dict('os.environ', {'FSLDIR': 'some_value'}): - with patch('os.path.isdir', side_effect=[True, False]): - with pytest.raises(ValueError, match=f"Directory '{input_dir}' is missing."): - create_tracts(samples_dir, input_dir) - - -def test_connectivity_driven(): - # Mocking the environment variable - with patch.dict('os.environ', {'FSLDIR': 'some_value'}): - # Mocking the os.path.isfile function to always return True - with patch('os.path.isfile', return_value=True): - # Mocking the subprocess.run function to do nothing - with patch('subprocess.run') as mock_subprocess: - target1 = "some_target1_path" - target2 = "some_target2_path" - out = "some_out_path" - connectivity_driven(target1, target2, out) - mock_subprocess.assert_called_once() - - # Testing for missing FSLDIR environment variable - with patch.dict('os.environ', {}, clear=True): - with pytest.raises(ValueError, match="FSLDIR environment variable is missing."): - connectivity_driven(target1, target2, out) - - # Testing for missing target1 file - with patch.dict('os.environ', {'FSLDIR': 'some_value'}): - with patch('os.path.isfile', side_effect=[False, True]): - with pytest.raises(ValueError, match=f"{target1} does not exist."): - connectivity_driven(target1, target2, out) - - # Testing for missing target2 file - with patch.dict('os.environ', {'FSLDIR': 'some_value'}): - with patch('os.path.isfile', side_effect=[True, False]): - with pytest.raises(ValueError, match=f"{target2} does not exist."): - connectivity_driven(target1, target2, out) \ No newline at end of file diff --git a/tests/test_utils.py b/tests/test_utils.py index 04976a90569755500ed02f5613c5a2be2a41fb7d..201e352e8f3e8fc448c37f0db9204fe8dab8022b 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,8 +1,7 @@ -import os, pytest +import os import numpy as np import subprocess -from localise.utils import save_nifti, save_nifti_4D, get_subjects -from localise.utils import predict_mode, train_mode +from localise.utils import save_nifti, save_nifti_4D from localise.utils import run_command from pathlib import Path import nibabel as nib @@ -38,81 +37,6 @@ def test_save_nifti_4D(): for k in range(2): saved_data_slice = saved_data[:, :, :, k] assert np.allclose(saved_data_slice[mask_data != 0], vectors[:, k], atol=1e-6, rtol=1e-5) - - -def test_get_subjects(tmp_path): - # Test with file - d = tmp_path / "subdir" - d.mkdir() - p = d / "subjects.txt" - p.write_text("subject1\nsubject2\n") - - result = get_subjects(str(p)) - assert result == ["subject1", "subject2"] - - # Test with directory - result = get_subjects(str(d)) - assert result == [str(d)] - - # Test with invalid path - with pytest.raises(ValueError): - get_subjects(str(tmp_path / "nonexistent")) - - -def test_predict_mode(): - subject = f'{path_to_data}/100206' - mask = 'roi/left/tha_small.nii.gz' - target_path = 'streamlines/left' - target_list = f'{path_to_data}/models/targets_list113_left.txt' - atlas = 'roi/left/atlas.nii.gz' - out = 'roi/left/prediction.nii.gz' - model = f'{path_to_data}/models/vim_spatial_model.pth' - - predict_mode(subject=subject, mask=mask, target_path=target_path, - target_list=target_list,atlas=atlas,out=out,model=model) - assert os.path.isfile(os.path.join(subject, out)) - os.remove(os.path.join(subject, out)) - - predict_mode(subject=subject, mask=mask, structure='vim', target_path=target_path, - atlas=atlas, out=out, data_type='single32') - assert os.path.isfile(os.path.join(subject, out)) - os.remove(os.path.join(subject, out)) - - with pytest.raises(ValueError): - predict_mode(subject=subject, mask=mask, target_path=target_path, - atlas=atlas, out=out) - - with pytest.raises(ValueError): - predict_mode(subject=subject, mask=mask, structure='vim', target_path=target_path, - atlas=atlas, out=out) - - predict_mode(subject=subject, mask=mask, structure='vim', target_path=target_path, - target_list=target_list, atlas=atlas, out=out, data_type='single32') - - assert os.path.isfile(os.path.join(subject, out)) - os.remove(os.path.join(subject, out)) - - predict_mode(subject=subject, mask=mask, data='streamlines/left/X113_small_1mm.npy', - structure='vim', spatial=False, - atlas=atlas, out=out, data_type='single32') - - assert os.path.isfile(os.path.join(subject, out)) - os.remove(os.path.join(subject, out)) - -def test_train_mode(): - subject = f'{path_to_data}/100206' - mask = 'roi/left/tha_small.nii.gz' - label = 'high-quality-labels/left/labels.nii.gz' - target_path = 'streamlines/left' - target_list = f'{path_to_data}/models/targets_list113_left.txt' - atlas = 'roi/left/atlas.nii.gz' - out_model = f'{path_to_data}/models/test_model.pth' - - train_mode(subject=subject, mask=mask, label=label, target_path=target_path, - target_list=target_list, atlas=atlas, out_model=out_model) - - assert os.path.isfile(out_model) - os.remove(out_model) def test_run_command(): # Test successful command execution