diff --git a/fsl/utils/filetree/filetree.py b/fsl/utils/filetree/filetree.py index fb7aa082f47f432666feed07b00474c3c5c23d70..69c3d75b0c039e06d2d9e9e349763aa8e5532f73 100644 --- a/fsl/utils/filetree/filetree.py +++ b/fsl/utils/filetree/filetree.py @@ -185,7 +185,7 @@ class FileTree(object): """ return tuple(self.extract_variables(short_name, fn) for fn in self.get_all(short_name, glob_vars=glob_vars)) - def get_all_trees(self, short_name: str, global_vars=()) -> Tuple["FileTree"]: + def get_all_trees(self, short_name: str, glob_vars=()) -> Tuple["FileTree"]: """ Gets all the trees that generate the existing files matching the pattern @@ -197,7 +197,7 @@ class FileTree(object): If glob_vars is set to 'all', all undefined variables will be used to look up matches. :return: sequence of FileTrees used to generate each file on disk matching the pattern of `short_name` """ - return tuple(self.update(**vars) for vars in self.get_all_vars(short_name, glob_vars=global_vars)) + return tuple(self.update(**vars) for vars in self.get_all_vars(short_name, glob_vars=glob_vars)) def update(self, **variables) -> "FileTree": """ diff --git a/fsl/utils/filetree/trees/HCP_Surface.tree b/fsl/utils/filetree/trees/HCP_Surface.tree index 7850b8db7ff488c38674ab6e6d9d5514258fe980..0d6e025390a7eb71b697e3011d7edea4ecb5693b 100644 --- a/fsl/utils/filetree/trees/HCP_Surface.tree +++ b/fsl/utils/filetree/trees/HCP_Surface.tree @@ -17,6 +17,9 @@ {subject}.{hemi}.sphere.reg.reg_LR.native.surf.gii (sphere_reg_LR) {subject}.{hemi}.sphere.MSMSulc.native.surf.gii (sphere_MSMSulc) {subject}.{hemi}.sphere.MSMAll.native.surf.gii (sphere_msm) +{subject}.{hemi}.BA.32k_fs_LR.label.gii (BA_gifti) +{subject}.{hemi}.aparc.32k_fs_LR.label.gii (aparc_gifti) +{subject}.{hemi}.aparc.a2009s.32k_fs_LR.label.gii (aparc2009_gifti) {subject}.{space}.wb.spec (spec) {subject}.sulc.{space}.dscalar.nii (sulc_cifti) {subject}.thickness.{space}.dscalar.nii (thick_cifti) @@ -24,3 +27,6 @@ {subject}.sulc_MSMAll.{space}.dscalar.nii (sulc_msm_cifti) {subject}.thickness_MSMAll.{space}.dscalar.nii (thick_msm_cifti) {subject}.curvature_MSMAll.{space}.dscalar.nii (curv_msm_cifti) +{subject}.BA.32k_fs_LR.dlabel.nii (BA_cifti)) +{subject}.aparc.32k_fs_LR.dlabel.nii (aparc_cifti) +{subject}.aparc.a2009s.32k_fs_LR.dlabel.nii (aparc2009_cifti) diff --git a/fsl/utils/filetree/trees/HCP_directory.tree b/fsl/utils/filetree/trees/HCP_directory.tree index 11c1ec5eb00767c802dd98daede9f5fe2a193123..3e69fb7aac59f7427fe4f561ef8302d93c47a2d4 100644 --- a/fsl/utils/filetree/trees/HCP_directory.tree +++ b/fsl/utils/filetree/trees/HCP_directory.tree @@ -24,6 +24,11 @@ NonlinearRegJacobians.nii.gz acpc_dc2standard.nii.gz standard2acpc_dc.nii.gz + Results + rfMRI_REST{run_id}_{phase_encoding} + Movement_RelativeRMS_mean.txt + rfMRI_REST{run_id}_{phase_encoding}_Atlas_MSMAll_hp2000_clean.dtseries.nii (resting_cifti) + rfMRI_REST{run_id}_{phase_encoding}_hp2000_clean.nii.gz (resting_nifti) T1w (acpc_dc) Diffusion ->Diffusion (Diffusion)