Commit c4304366 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

ENH: cluster submission

parent 295d2e89
...@@ -34,7 +34,8 @@ ...@@ -34,7 +34,8 @@
" * [The `fslmaths` wrapper](#the-fslmaths-wrapper)\n", " * [The `fslmaths` wrapper](#the-fslmaths-wrapper)\n",
"* [The `filetree`](#the-filetree)\n", "* [The `filetree`](#the-filetree)\n",
"* [Calling shell commands](#calling-shell-commands)\n", "* [Calling shell commands](#calling-shell-commands)\n",
" * [`runfsl` and `submit`](#runfsl-and-submit)\n", " * [The `runfsl` function](#the-runfsl-function)\n",
" * [Submitting to the cluster](#submitting-to-the-cluster)\n",
" * [Redirecting output](#redirecting-output)\n", " * [Redirecting output](#redirecting-output)\n",
"* [FSL atlases](#fsl-atlases)\n", "* [FSL atlases](#fsl-atlases)\n",
" * [Querying atlases](#querying-atlases)\n", " * [Querying atlases](#querying-atlases)\n",
...@@ -711,6 +712,10 @@ ...@@ -711,6 +712,10 @@
"constructing a command-line, or saving/loading input/output images.\n", "constructing a command-line, or saving/loading input/output images.\n",
"\n", "\n",
"\n", "\n",
"> The `fsl.wrappers` functions also allow you to submit jobs to be run on the\n",
"> cluster - this is described [below](#submitting-to-the-cluster).\n",
"\n",
"\n",
"You can use the FSL wrapper functions with file names, similar to calling the\n", "You can use the FSL wrapper functions with file names, similar to calling the\n",
"corresponding tool via the command-line:" "corresponding tool via the command-line:"
] ]
...@@ -732,7 +737,7 @@ ...@@ -732,7 +737,7 @@
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"The `fsl.wrapper` functions strive to provide an interface which is as close\n", "The `fsl.wrappers` functions strive to provide an interface which is as close\n",
"as possible to the command-line tool - most functions use positional arguments\n", "as possible to the command-line tool - most functions use positional arguments\n",
"for required options, and keyword arguments for all other options, with\n", "for required options, and keyword arguments for all other options, with\n",
"argument names equivalent to command line option names. For example, the usage\n", "argument names equivalent to command line option names. For example, the usage\n",
...@@ -793,9 +798,9 @@ ...@@ -793,9 +798,9 @@
"\n", "\n",
"\n", "\n",
"It can be quite awkward to combine image processing with FSL tools and image\n", "It can be quite awkward to combine image processing with FSL tools and image\n",
"processing in Python. The `fsl.wrapper` package tries to make this a little\n", "processing in Python. The `fsl.wrappers` package tries to make this a little\n",
"easier for you - if you are working with image data in Python, you can pass\n", "easier for you - if you are working with image data in Python, you can pass\n",
"`Image` or `nibabel` objects directly into `fsl.wrapper` functions - they will\n", "`Image` or `nibabel` objects directly into `fsl.wrappers` functions - they will\n",
"be automatically saved to temporary files and passed to the underlying FSL\n", "be automatically saved to temporary files and passed to the underlying FSL\n",
"command:" "command:"
] ]
...@@ -824,8 +829,8 @@ ...@@ -824,8 +829,8 @@
"### Loading outputs into Python\n", "### Loading outputs into Python\n",
"\n", "\n",
"\n", "\n",
"By using the special `fsl.wrappers.LOAD` symbol, you can have any output\n", "By using the special `fsl.wrappers.LOAD` symbol, you can also have any output\n",
"files produced by the tool automatically loaded in too:" "files produced by the tool automatically loaded:"
] ]
}, },
{ {
...@@ -877,9 +882,9 @@ ...@@ -877,9 +882,9 @@
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"For tools like `bet`, which expect an output *prefix* or *basename*, you can\n", "For tools like `bet` and `fast`, which expect an output *prefix* or\n",
"just set the prefix to `LOAD` - all output files with that prefix will be\n", "*basename*, you can just set the prefix to `LOAD` - all output files with that\n",
"available in the returned dictionary:" "prefix will be available in the returned dictionary:"
] ]
}, },
{ {
...@@ -906,7 +911,7 @@ ...@@ -906,7 +911,7 @@
"### The `fslmaths` wrapper\n", "### The `fslmaths` wrapper\n",
"\n", "\n",
"\n", "\n",
"*Most* of the `fsl.wrapper` functions aim to provide an interface which is as\n", "*Most* of the `fsl.wrappers` functions aim to provide an interface which is as\n",
"close as possible to the underlying FSL tool. Ideally, if you read the\n", "close as possible to the underlying FSL tool. Ideally, if you read the\n",
"command-line help for a tool, you should be able to figure out how to use the\n", "command-line help for a tool, you should be able to figure out how to use the\n",
"corresponding wrapper function. The wrapper for the `fslmaths` command is a\n", "corresponding wrapper function. The wrapper for the `fslmaths` command is a\n",
...@@ -964,6 +969,8 @@ ...@@ -964,6 +969,8 @@
"## The `filetree`\n", "## The `filetree`\n",
"\n", "\n",
"\n", "\n",
"todo\n",
"\n",
"\n", "\n",
"<a class=\"anchor\" id=\"calling-shell-commands\"></a>\n", "<a class=\"anchor\" id=\"calling-shell-commands\"></a>\n",
"## Calling shell commands\n", "## Calling shell commands\n",
...@@ -1096,8 +1103,8 @@ ...@@ -1096,8 +1103,8 @@
"cell_type": "markdown", "cell_type": "markdown",
"metadata": {}, "metadata": {},
"source": [ "source": [
"<a class=\"anchor\" id=\"runfsl-and-submit\"></a>\n", "<a class=\"anchor\" id=\"the-runfsl-function\"></a>\n",
"### `runfsl` and `submit`\n", "### The `runfsl` function\n",
"\n", "\n",
"\n", "\n",
"The `runfsl` function is a wrapper around `run` which simply makes sure that\n", "The `runfsl` function is a wrapper around `run` which simply makes sure that\n",
...@@ -1112,8 +1119,125 @@ ...@@ -1112,8 +1119,125 @@
"outputs": [], "outputs": [],
"source": [ "source": [
"from fsl.utils.run import runfsl\n", "from fsl.utils.run import runfsl\n",
"runfsl('fslroi 08_fslpy/bighead_cropped bighead_slices 0 -1 0 -1 90 5')\n", "runfsl('bet 08_fslpy/bighead_cropped bighead_cropped_brain')\n",
"runfsl('fast -o bighead_fast bighead_slices')" "runfsl('fslroi bighead_cropped_brain bighead_slices 0 -1 0 -1 90 3')\n",
"runfsl('fast -o bighead_fast bighead_slices')\n",
"\n",
"render('-vl 80 112 91 -xh -yh '\n",
" '08_fslpy/bighead_cropped '\n",
" 'bighead_slices.nii.gz -cm brain_colours_1hot -b 30 '\n",
" 'bighead_fast_seg.nii.gz -ot label -o')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<a class=\"anchor\" id=\"submitting-to-the-cluster\"></a>\n",
"### Submitting to the cluster\n",
"\n",
"\n",
"Both the `run` and `runfsl` accept an argument called `submit`, which allows\n",
"you to submit jobs to be executed on the cluster via the FSL `fsl_sub`\n",
"command.\n",
"\n",
"\n",
"> Cluster submission is handled by the\n",
"> [`fsl.utils.fslsub`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.fslsub.html)\n",
"> module - it contains lower level functions for managing and querying jobs\n",
"> that have been submitted to the cluster. The functions defined in this\n",
"> module can be used directly if you have more complicated requirements.\n",
"\n",
"\n",
"The semantics of the `run` and `runfsl` functions are slightly different when\n",
"you use the `submit` option - when you submit a job, the `run`/`runfsl` will\n",
"return immediately, and will return a string containing the job ID:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"jobid = run('ls', submit=True)\n",
"print('Job ID:', jobid)\n",
"stdout = f'ls.o{jobid}'\n",
"print('Job output')\n",
"print(open(stdout).read())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"All of the `fsl.wrappers` functions also accept the `submit` argument:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"jobid = bet('08_fslpy/bighead', 'bighead_brain', submit=True)\n",
"print('Job ID:', jobid)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"> But an error will occur if you try to pass in-memory images, or `LOAD` any\n",
"> outputs when you call a wrapper function with `submit=True`.\n",
"\n",
"\n",
"After submitting a job, you can use the `wait` function to wait until a job\n",
"has completed:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from fsl.utils.run import wait\n",
"jobid = bet('08_fslpy/bighead', 'bighead_brain', submit=True)\n",
"print('Job ID:', jobid)\n",
"wait(jobid)\n",
"print('Done!')\n",
"render('08_fslpy/bighead bighead_brain -cm hot')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"When you submit a job, instead of passing `submit=True`, you can pass in a\n",
"dict which contains cluster submission options - you can include any arguments\n",
"to the\n",
"[`fslsub.submit`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.fslsub.html#fsl.utils.fslsub.submit)\n",
"function:"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"jid = runfsl('robustfov -i 08_fslpy/bighead -r bighead_cropped', submit=dict(queue='short.q'))\n",
"jid = runfsl('bet bighead_cropped bighead_brain', submit=dict(queue='short.q', wait_for=jid))\n",
"jid = runfsl('fslroi bighead_brain bighead_slices 0 -1 111 3 0 -1', submit=dict(queue='short.q', wait_for=jid))\n",
"jid = runfsl('fast -o bighead_fast bighead_slices', submit=dict(queue='short.q', wait_for=jid))\n",
"\n",
"wait(jid)\n",
"\n",
"render('-vl 80 112 91 -xh -zh -hc '\n",
" 'bighead_brain '\n",
" 'bighead_slices.nii.gz -cm brain_colours_1hot -b 30 '\n",
" 'bighead_fast_seg.nii.gz -ot label -o')"
] ]
}, },
{ {
......
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
# `fslpy` # `fslpy`
[`fslpy`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/) is a [`fslpy`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/) is a
Python library which is built into FSL, and contains a range of functionality Python library which is built into FSL, and contains a range of functionality
for working with neuroimaging data from Python. for working with neuroimaging data from Python.
This practical highlights some of the most useful features provided by This practical highlights some of the most useful features provided by
`fslpy`. You may find `fslpy` useful if you are writing Python code to `fslpy`. You may find `fslpy` useful if you are writing Python code to
perform analyses and image processing in conjunction with FSL. perform analyses and image processing in conjunction with FSL.
> **Note**: `fslpy` is distinct from `fslpython` - `fslpython` is the Python > **Note**: `fslpy` is distinct from `fslpython` - `fslpython` is the Python
> environment that is baked into FSL. `fslpy` is a Python library which is > environment that is baked into FSL. `fslpy` is a Python library which is
> installed into the `fslpython` environment. > installed into the `fslpython` environment.
* [The `Image` class, and other data types](#the-image-class-and-other-data-types) * [The `Image` class, and other data types](#the-image-class-and-other-data-types)
* [Creating images](#creating-images) * [Creating images](#creating-images)
* [Working with image data](#working-with-image-data) * [Working with image data](#working-with-image-data)
* [Loading other file types](#loading-other-file-types) * [Loading other file types](#loading-other-file-types)
* [NIfTI coordinate systems](#nifti-coordinate-systems) * [NIfTI coordinate systems](#nifti-coordinate-systems)
* [Image processing](#image-processing) * [Image processing](#image-processing)
* [FSL wrapper functions](#fsl-wrapper-functions) * [FSL wrapper functions](#fsl-wrapper-functions)
* [In-memory images](#in-memory-images) * [In-memory images](#in-memory-images)
* [Loading outputs into Python](#loading-outputs-into-python) * [Loading outputs into Python](#loading-outputs-into-python)
* [The `fslmaths` wrapper](#the-fslmaths-wrapper) * [The `fslmaths` wrapper](#the-fslmaths-wrapper)
* [The `filetree`](#the-filetree) * [The `filetree`](#the-filetree)
* [Calling shell commands](#calling-shell-commands) * [Calling shell commands](#calling-shell-commands)
* [`runfsl` and `submit`](#runfsl-and-submit) * [The `runfsl` function](#the-runfsl-function)
* [Submitting to the cluster](#submitting-to-the-cluster)
* [Redirecting output](#redirecting-output) * [Redirecting output](#redirecting-output)
* [FSL atlases](#fsl-atlases) * [FSL atlases](#fsl-atlases)
* [Querying atlases](#querying-atlases) * [Querying atlases](#querying-atlases)
* [Loading atlas images](#loading-atlas-images) * [Loading atlas images](#loading-atlas-images)
* [Working with atlases](#working-with-atlases) * [Working with atlases](#working-with-atlases)
Let's start with some standard imports and environment set-up: Let's start with some standard imports and environment set-up:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
%matplotlib inline %matplotlib inline
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import os import os
import os.path as op import os.path as op
import nibabel as nib import nibabel as nib
import numpy as np import numpy as np
import warnings import warnings
warnings.filterwarnings("ignore") warnings.filterwarnings("ignore")
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
And a little function that we can use to generate a simple orthographic plot: And a little function that we can use to generate a simple orthographic plot:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
def ortho(data, voxel, fig=None, **kwargs): def ortho(data, voxel, fig=None, **kwargs):
"""Simple orthographic plot of a 3D array using matplotlib. """Simple orthographic plot of a 3D array using matplotlib.
:arg data: 3D numpy array :arg data: 3D numpy array
:arg voxel: XYZ coordinates for each slice :arg voxel: XYZ coordinates for each slice
:arg fig: Existing figure and axes for overlay plotting :arg fig: Existing figure and axes for overlay plotting
All other arguments are passed through to the `imshow` function. All other arguments are passed through to the `imshow` function.
:returns: The figure and axes (which can be passed back in as the :returns: The figure and axes (which can be passed back in as the
`fig` argument to plot overlays). `fig` argument to plot overlays).
""" """
data = np.asanyarray(data, dtype=np.float) data = np.asanyarray(data, dtype=np.float)
data[data <= 0] = np.nan data[data <= 0] = np.nan
x, y, z = voxel x, y, z = voxel
xslice = np.flipud(data[x, :, :].T) xslice = np.flipud(data[x, :, :].T)
yslice = np.flipud(data[:, y, :].T) yslice = np.flipud(data[:, y, :].T)
zslice = np.flipud(data[:, :, z].T) zslice = np.flipud(data[:, :, z].T)
if fig is None: if fig is None:
fig = plt.figure() fig = plt.figure()
xax = fig.add_subplot(1, 3, 1) xax = fig.add_subplot(1, 3, 1)
yax = fig.add_subplot(1, 3, 2) yax = fig.add_subplot(1, 3, 2)
zax = fig.add_subplot(1, 3, 3) zax = fig.add_subplot(1, 3, 3)
else: else:
fig, xax, yax, zax = fig fig, xax, yax, zax = fig
xax.imshow(xslice, **kwargs) xax.imshow(xslice, **kwargs)
yax.imshow(yslice, **kwargs) yax.imshow(yslice, **kwargs)
zax.imshow(zslice, **kwargs) zax.imshow(zslice, **kwargs)
for ax in (xax, yax, zax): for ax in (xax, yax, zax):
ax.set_xticks([]) ax.set_xticks([])
ax.set_yticks([]) ax.set_yticks([])
fig.tight_layout(pad=0) fig.tight_layout(pad=0)
return (fig, xax, yax, zax) return (fig, xax, yax, zax)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
And another function which uses FSLeyes for more complex plots: And another function which uses FSLeyes for more complex plots:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
import shlex import shlex
import IPython.display as display import IPython.display as display
from fsleyes.render import main from fsleyes.render import main
def render(cmdline): def render(cmdline):
prefix = '-of screenshot.png -hl -c 2 ' prefix = '-of screenshot.png -hl -c 2 '
main(shlex.split(prefix + cmdline)) main(shlex.split(prefix + cmdline))
return display.Image('screenshot.png') return display.Image('screenshot.png')
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
<a class="anchor" id="the-image-class-and-other-data-types"></a> <a class="anchor" id="the-image-class-and-other-data-types"></a>
## The `Image` class, and other data types ## The `Image` class, and other data types
The The
[`fsl.data.image`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.image.html#fsl.data.image.Image) [`fsl.data.image`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.image.html#fsl.data.image.Image)
module provides the `Image` class, which sits on top of `nibabel` and contains module provides the `Image` class, which sits on top of `nibabel` and contains
some handy functionality if you need to work with coordinate transformations, some handy functionality if you need to work with coordinate transformations,
or do some FSL-specific processing. The `Image` class provides features such or do some FSL-specific processing. The `Image` class provides features such
as: as:
- Support for NIFTI1, NIFTI2, and ANALYZE image files - Support for NIFTI1, NIFTI2, and ANALYZE image files
- Access to affine transformations between the voxel, FSL and world coordinate - Access to affine transformations between the voxel, FSL and world coordinate
systems systems
- Ability to load metadata from BIDS sidecar files - Ability to load metadata from BIDS sidecar files
Some simple image processing routines are also provided - these are covered Some simple image processing routines are also provided - these are covered
[below](#image-processing). [below](#image-processing).
<a class="anchor" id="creating-images"></a> <a class="anchor" id="creating-images"></a>
### Creating images ### Creating images
It's easy to create an `Image` - you can create one from a file name: It's easy to create an `Image` - you can create one from a file name:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
from fsl.data.image import Image from fsl.data.image import Image
stddir = op.expandvars('${FSLDIR}/data/standard/') stddir = op.expandvars('${FSLDIR}/data/standard/')
# load a FSL image - the file # load a FSL image - the file
# suffix is optional, just like # suffix is optional, just like
# in real FSL-land! # in real FSL-land!
img = Image(op.join(stddir, 'MNI152_T1_1mm')) img = Image(op.join(stddir, 'MNI152_T1_1mm'))
print(img) print(img)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
You can create an `Image` from an existing `nibabel` image: You can create an `Image` from an existing `nibabel` image:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
# load a nibabel image, and # load a nibabel image, and
# convert it into an FSL image # convert it into an FSL image
nibimg = nib.load(op.join(stddir, 'MNI152_T1_1mm.nii.gz')) nibimg = nib.load(op.join(stddir, 'MNI152_T1_1mm.nii.gz'))
img = Image(nibimg) img = Image(nibimg)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Or you can create an `Image` from a `numpy` array: Or you can create an `Image` from a `numpy` array:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
data = np.zeros((100, 100, 100)) data = np.zeros((100, 100, 100))
img = Image(data, xform=np.eye(4)) img = Image(data, xform=np.eye(4))
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
You can save an image to file via the `save` method: You can save an image to file via the `save` method:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
img.save('empty.nii.gz') img.save('empty.nii.gz')
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
`Image` objects have all of the attributes you might expect: `Image` objects have all of the attributes you might expect:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
stddir = op.expandvars('${FSLDIR}/data/standard/') stddir = op.expandvars('${FSLDIR}/data/standard/')
std1mm = Image(op.join(stddir, 'MNI152_T1_1mm')) std1mm = Image(op.join(stddir, 'MNI152_T1_1mm'))
print('name: ', std1mm.name) print('name: ', std1mm.name)
print('file: ', std1mm.dataSource) print('file: ', std1mm.dataSource)
print('NIfTI version:', std1mm.niftiVersion) print('NIfTI version:', std1mm.niftiVersion)
print('ndim: ', std1mm.ndim) print('ndim: ', std1mm.ndim)
print('shape: ', std1mm.shape) print('shape: ', std1mm.shape)
print('dtype: ', std1mm.dtype) print('dtype: ', std1mm.dtype)
print('nvals: ', std1mm.nvals) print('nvals: ', std1mm.nvals)
print('pixdim: ', std1mm.pixdim) print('pixdim: ', std1mm.pixdim)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
and a number of useful methods: and a number of useful methods:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
std2mm = Image(op.join(stddir, 'MNI152_T1_2mm')) std2mm = Image(op.join(stddir, 'MNI152_T1_2mm'))
mask2mm = Image(op.join(stddir, 'MNI152_T1_2mm_brain_mask')) mask2mm = Image(op.join(stddir, 'MNI152_T1_2mm_brain_mask'))
print(std1mm.sameSpace(std2mm)) print(std1mm.sameSpace(std2mm))
print(std2mm.sameSpace(mask2mm)) print(std2mm.sameSpace(mask2mm))
print(std2mm.getAffine('voxel', 'world')) print(std2mm.getAffine('voxel', 'world'))
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
An `Image` object is a high-level wrapper around a `nibabel` image object - An `Image` object is a high-level wrapper around a `nibabel` image object -
you can always work directly with the `nibabel` object via the `nibImage` you can always work directly with the `nibabel` object via the `nibImage`
attribute: attribute:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
print(std2mm) print(std2mm)
print(std2mm.nibImage) print(std2mm.nibImage)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
<a class="anchor" id="working-with-image-data"></a> <a class="anchor" id="working-with-image-data"></a>
### Working with image data ### Working with image data
You can get the image data as a `numpy` array via the `data` attribute: You can get the image data as a `numpy` array via the `data` attribute:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
data = std2mm.data data = std2mm.data
print(data.min(), data.max()) print(data.min(), data.max())
ortho(data, (45, 54, 45)) ortho(data, (45, 54, 45))
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
> Note that `Image.data` will give you the data in its underlying type, unlike > Note that `Image.data` will give you the data in its underlying type, unlike
> the `nibabel.get_fdata` method, which up-casts image data to floating-point. > the `nibabel.get_fdata` method, which up-casts image data to floating-point.
You can also read and write data directly via the `Image` object: You can also read and write data directly via the `Image` object:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
slc = std2mm[:, :, 45] slc = std2mm[:, :, 45]
std2mm[0:10, :, :] *= 2 std2mm[0:10, :, :] *= 2
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Doing so has some advantages that may or may not be useful, depending on your Doing so has some advantages that may or may not be useful, depending on your
use-case: use-case:
- The image data will be kept on disk - only the parts that you access will - The image data will be kept on disk - only the parts that you access will
be loaded into RAM (you will also need to pass`loadData=False` when creating be loaded into RAM (you will also need to pass`loadData=False` when creating
the `Image` to achieve this). the `Image` to achieve this).
- The `Image` object will keep track of modifications to the data - this can - The `Image` object will keep track of modifications to the data - this can
be queried via the `saveState` attribute. be queried via the `saveState` attribute.
<a class="anchor" id="loading-other-file-types"></a> <a class="anchor" id="loading-other-file-types"></a>
### Loading other file types ### Loading other file types
The The
[`fsl.data`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.html#module-fsl.data) [`fsl.data`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.html#module-fsl.data)
package has a number of other classes for working with different types of FSL package has a number of other classes for working with different types of FSL
and neuroimaging data. Most of these are higher-level wrappers around the and neuroimaging data. Most of these are higher-level wrappers around the
corresponding `nibabel` types: corresponding `nibabel` types:
* The * The
[`fsl.data.bitmap.Bitmap`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.bitmap.html) [`fsl.data.bitmap.Bitmap`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.bitmap.html)
class can be used to load a bitmap image (e.g. `jpg, `png`, etc) and class can be used to load a bitmap image (e.g. `jpg, `png`, etc) and
convert it to a NIfTI image. convert it to a NIfTI image.
* The * The
[`fsl.data.dicom.DicomImage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.dicom.html) [`fsl.data.dicom.DicomImage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.dicom.html)
class uses `dcm2niix` to load NIfTI images contained within a DICOM class uses `dcm2niix` to load NIfTI images contained within a DICOM
directory<sup>*</sup>. directory<sup>*</sup>.
* The * The
[`fsl.data.mghimahe.MGHImage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.mghimage.html) [`fsl.data.mghimahe.MGHImage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.mghimage.html)
class can be used too load `.mgh`/`.mgz` images (they are converted into class can be used too load `.mgh`/`.mgz` images (they are converted into
NIfTI images). NIfTI images).
* The * The
[`fsl.data.dtifit`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.dtifit.html) [`fsl.data.dtifit`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.dtifit.html)
module contains functions for loading and working with the output of the module contains functions for loading and working with the output of the
FSL `dtifit` tool. FSL `dtifit` tool.
* The * The
[`fsl.data.featanalysis`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.featanalysis.html), [`fsl.data.featanalysis`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.featanalysis.html),
[`fsl.data.featimage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.featimage.html), [`fsl.data.featimage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.featimage.html),
and and
[`fsl.data.featdesign`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.featdesign.html) [`fsl.data.featdesign`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.featdesign.html)
modules contain classes and functions for loading data from FEAT modules contain classes and functions for loading data from FEAT
directories. directories.
* Similarly, the * Similarly, the
[`fsl.data.melodicanalysis`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.melodicanalysis.html) [`fsl.data.melodicanalysis`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.melodicanalysis.html)
and and
[`fsl.data.melodicimage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.melodicimage.html) [`fsl.data.melodicimage`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.melodicimage.html)
modules contain classes and functions for loading data from MELODIC modules contain classes and functions for loading data from MELODIC
directories. directories.
* The * The
[`fsl.data.gifti`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.gifti.html), [`fsl.data.gifti`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.gifti.html),
[`fsl.data.freesurfer`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.freesurfer.html), [`fsl.data.freesurfer`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.freesurfer.html),
and and
[`fsl.data.vtk`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.vtk.html) [`fsl.data.vtk`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.vtk.html)
modules contain functionality form loading surface data from GIfTI, modules contain functionality form loading surface data from GIfTI,
freesurfer, and VTK files respectively. freesurfer, and VTK files respectively.
> <sup>*</sup>You must make sure that `dcm2niix` is installed on your system > <sup>*</sup>You must make sure that `dcm2niix` is installed on your system
> in order to use this class. > in order to use this class.
<a class="anchor" id="nifti-coordinate-systems"></a> <a class="anchor" id="nifti-coordinate-systems"></a>
### NIfTI coordinate systems ### NIfTI coordinate systems
The `Image.getAffine` method gives you access to affine transformations which The `Image.getAffine` method gives you access to affine transformations which
can be used to convert coordinates between the different coordinate systems can be used to convert coordinates between the different coordinate systems
associated with a NIfTI image. Have some MNI coordinates you'd like to convert associated with a NIfTI image. Have some MNI coordinates you'd like to convert
to voxels? Easy! to voxels? Easy!
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
stddir = op.expandvars('${FSLDIR}/data/standard/') stddir = op.expandvars('${FSLDIR}/data/standard/')
std2mm = Image(op.join(stddir, 'MNI152_T1_2mm')) std2mm = Image(op.join(stddir, 'MNI152_T1_2mm'))
mnicoords = np.array([[0, 0, 0], mnicoords = np.array([[0, 0, 0],
[0, -18, 18]]) [0, -18, 18]])
world2vox = std2mm.getAffine('world', 'voxel') world2vox = std2mm.getAffine('world', 'voxel')
vox2world = std2mm.getAffine('voxel', 'world') vox2world = std2mm.getAffine('voxel', 'world')
# Apply the world->voxel # Apply the world->voxel
# affine to the coordinates # affine to the coordinates
voxcoords = (np.dot(world2vox[:3, :3], mnicoords.T)).T + world2vox[:3, 3] voxcoords = (np.dot(world2vox[:3, :3], mnicoords.T)).T + world2vox[:3, 3]
# The code above is a bit fiddly, so # The code above is a bit fiddly, so
# instead of figuring it out, you can # instead of figuring it out, you can
# just use the transform() function: # just use the transform() function:
from fsl.transform.affine import transform from fsl.transform.affine import transform
voxcoords = transform(mnicoords, world2vox) voxcoords = transform(mnicoords, world2vox)
# just to double check, let's transform # just to double check, let's transform
# those voxel coordinates back into world # those voxel coordinates back into world
# coordinates # coordinates
backtomni = transform(voxcoords, vox2world) backtomni = transform(voxcoords, vox2world)
for m, v, b in zip(mnicoords, voxcoords, backtomni): for m, v, b in zip(mnicoords, voxcoords, backtomni):
print(m, '->', v, '->', b) print(m, '->', v, '->', b)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
> The `Image.getAffine` method can give you transformation matrices > The `Image.getAffine` method can give you transformation matrices
> between any of these coordinate systems: > between any of these coordinate systems:
> >
> - `'voxel'`: Image data voxel coordinates > - `'voxel'`: Image data voxel coordinates
> - `'world'`: mm coordinates, defined by the sform/qform of an image > - `'world'`: mm coordinates, defined by the sform/qform of an image
> - `'fsl'`: The FSL coordinate system, used internally by many FSL tools > - `'fsl'`: The FSL coordinate system, used internally by many FSL tools
> (e.g. FLIRT) > (e.g. FLIRT)
Oh, that example was too easy I hear you say? Try this one on for size. Let's Oh, that example was too easy I hear you say? Try this one on for size. Let's
say we have run FEAT on some task fMRI data, and want to get the MNI say we have run FEAT on some task fMRI data, and want to get the MNI
coordinates of the voxel with peak activation. coordinates of the voxel with peak activation.
> This is what people used to use `Featquery` for, back in the un-enlightened > This is what people used to use `Featquery` for, back in the un-enlightened
> days. > days.
Let's start by identifying the voxel with the biggest t-statistic: Let's start by identifying the voxel with the biggest t-statistic:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
featdir = op.join('08_fslpy', 'fmri.feat') featdir = op.join('08_fslpy', 'fmri.feat')
tstat1 = Image(op.join(featdir, 'stats', 'tstat1')).data tstat1 = Image(op.join(featdir, 'stats', 'tstat1')).data
# Recall from the numpy practical that # Recall from the numpy practical that
# argmax gives us a 1D index into a # argmax gives us a 1D index into a
# flattened view of the array. We can # flattened view of the array. We can
# use the unravel_index function to # use the unravel_index function to
# convert it into a 3D index. # convert it into a 3D index.
peakvox = np.abs(tstat1).argmax() peakvox = np.abs(tstat1).argmax()
peakvox = np.unravel_index(peakvox, tstat1.shape) peakvox = np.unravel_index(peakvox, tstat1.shape)
print('Peak voxel coordinates for tstat1:', peakvox, tstat1[peakvox]) print('Peak voxel coordinates for tstat1:', peakvox, tstat1[peakvox])
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Now that we've got the voxel coordinates in functional space, we need to Now that we've got the voxel coordinates in functional space, we need to
transform them into MNI space. FEAT provides a transformation which goes transform them into MNI space. FEAT provides a transformation which goes
directly from functional to standard space, in the `reg` directory: directly from functional to standard space, in the `reg` directory:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
func2std = np.loadtxt(op.join(featdir, 'reg', 'example_func2standard.mat')) func2std = np.loadtxt(op.join(featdir, 'reg', 'example_func2standard.mat'))
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
But ... wait a minute ... this is a FLIRT matrix! We can't just plug voxel But ... wait a minute ... this is a FLIRT matrix! We can't just plug voxel
coordinates into a FLIRT matrix and expect to get sensible results, because coordinates into a FLIRT matrix and expect to get sensible results, because
FLIRT works in an internal FSL coordinate system, which is not quite FLIRT works in an internal FSL coordinate system, which is not quite
`'voxel'`, and not quite `'world'`. So we need to do a little more work. `'voxel'`, and not quite `'world'`. So we need to do a little more work.
Let's start by loading our functional image, and the MNI152 template (the Let's start by loading our functional image, and the MNI152 template (the
source and reference images of our FLIRT matrix): source and reference images of our FLIRT matrix):
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
func = Image(op.join(featdir, 'reg', 'example_func')) func = Image(op.join(featdir, 'reg', 'example_func'))
std = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm'))) std = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm')))
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Now we can use them to get affines which convert between all of the different Now we can use them to get affines which convert between all of the different
coordinate systems - we're going to combine them into a single uber-affine, coordinate systems - we're going to combine them into a single uber-affine,
which transforms our functional-space voxels into MNI world coordinates via: which transforms our functional-space voxels into MNI world coordinates via:
1. functional voxels -> FLIRT source space 1. functional voxels -> FLIRT source space
2. FLIRT source space -> FLIRT reference space 2. FLIRT source space -> FLIRT reference space
3. FLIRT referece space -> MNI world coordinates 3. FLIRT referece space -> MNI world coordinates
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
vox2fsl = func.getAffine('voxel', 'fsl') vox2fsl = func.getAffine('voxel', 'fsl')
fsl2mni = std .getAffine('fsl', 'world') fsl2mni = std .getAffine('fsl', 'world')
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Combining two affines into one is just a simple dot-product. There is a Combining two affines into one is just a simple dot-product. There is a
`concat()` function which does this for us, for any number of affines: `concat()` function which does this for us, for any number of affines:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
from fsl.transform.affine import concat from fsl.transform.affine import concat
# To combine affines together, we # To combine affines together, we
# have to list them in reverse - # have to list them in reverse -
# linear algebra is *weird*. # linear algebra is *weird*.
funcvox2mni = concat(fsl2mni, func2std, vox2fsl) funcvox2mni = concat(fsl2mni, func2std, vox2fsl)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
So we've now got some voxel coordinates from our functional data, and an So we've now got some voxel coordinates from our functional data, and an
affine to transform into MNI world coordinates. The rest is easy: affine to transform into MNI world coordinates. The rest is easy:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
mnicoords = transform(peakvox, funcvox2mni) mnicoords = transform(peakvox, funcvox2mni)
mnivoxels = transform(mnicoords, std.getAffine('world', 'voxel')) mnivoxels = transform(mnicoords, std.getAffine('world', 'voxel'))
mnivoxels = [int(round(v)) for v in mnivoxels] mnivoxels = [int(round(v)) for v in mnivoxels]
print('Peak activation (MNI coordinates):', mnicoords) print('Peak activation (MNI coordinates):', mnicoords)
print('Peak activation (MNI voxels): ', mnivoxels) print('Peak activation (MNI voxels): ', mnivoxels)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
> Note that in the above example we are only applying a linear transformation > Note that in the above example we are only applying a linear transformation
> into MNI space - in reality you would also want to apply your non-linear > into MNI space - in reality you would also want to apply your non-linear
> structural-to-standard transformation too. But this is left as [an exercise > structural-to-standard transformation too. But this is left as [an exercise
> for the > for the
> reader](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.transform.fnirt.html). > reader](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.transform.fnirt.html).
<a class="anchor" id="image-processing"></a> <a class="anchor" id="image-processing"></a>
### Image processing ### Image processing
Now, it's all well and good to look at t-statistic values and voxel Now, it's all well and good to look at t-statistic values and voxel
coordinates and so on and so forth, but let's spice things up a bit and look coordinates and so on and so forth, but let's spice things up a bit and look
at some images. Let's display our peak activation location in MNI space. To do at some images. Let's display our peak activation location in MNI space. To do
this, we're going to resample our functional image into MNI space, so we can this, we're going to resample our functional image into MNI space, so we can
overlay it on the MNI template. This can be done using some handy functions overlay it on the MNI template. This can be done using some handy functions
from the from the
[`fsl.utils.image.resample`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.image.resample.html) [`fsl.utils.image.resample`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.image.resample.html)
module: module:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
from fsl.transform.flirt import fromFlirt from fsl.transform.flirt import fromFlirt
from fsl.utils.image.resample import resampleToReference from fsl.utils.image.resample import resampleToReference
featdir = op.join(op.join('08_fslpy', 'fmri.feat')) featdir = op.join(op.join('08_fslpy', 'fmri.feat'))
tstat1 = Image(op.join(featdir, 'stats', 'tstat1')) tstat1 = Image(op.join(featdir, 'stats', 'tstat1'))
std = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm'))) std = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm')))
# Load the func2standard FLIRT matrix, and adjust it # Load the func2standard FLIRT matrix, and adjust it
# so that it transforms from functional *world* # so that it transforms from functional *world*
# coordinates into standard *world* coordinates - # coordinates into standard *world* coordinates -
# this is what is expected by the resampleToReference # this is what is expected by the resampleToReference
# function, used below # function, used below
func2std = np.loadtxt(op.join(featdir, 'reg', 'example_func2standard.mat')) func2std = np.loadtxt(op.join(featdir, 'reg', 'example_func2standard.mat'))
func2std = fromFlirt(func2std, tstat1, std, 'world', 'world') func2std = fromFlirt(func2std, tstat1, std, 'world', 'world')
# All of the functions in the resample module # All of the functions in the resample module
# return a numpy array containing the resampled # return a numpy array containing the resampled
# data, and an adjusted voxel-to-world affine # data, and an adjusted voxel-to-world affine
# transformation. But when using the # transformation. But when using the
# resampleToReference function, the affine will # resampleToReference function, the affine will
# be the same as the MNI152 2mm affine, so we # be the same as the MNI152 2mm affine, so we
# can ignore it. # can ignore it.
std_tstat1 = resampleToReference(tstat1, std, func2std)[0] std_tstat1 = resampleToReference(tstat1, std, func2std)[0]
std_tstat1 = Image(std_tstat1, header=std.header) std_tstat1 = Image(std_tstat1, header=std.header)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Now that we have our t-statistic image in MNI152 space, we can plot it in Now that we have our t-statistic image in MNI152 space, we can plot it in
standard space using `matplotlib`: standard space using `matplotlib`:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
stddir = op.expandvars('${FSLDIR}/data/standard/') stddir = op.expandvars('${FSLDIR}/data/standard/')
std2mm = Image(op.join(stddir, 'MNI152_T1_2mm')) std2mm = Image(op.join(stddir, 'MNI152_T1_2mm'))
std_tstat1 = std_tstat1.data std_tstat1 = std_tstat1.data
std_tstat1[std_tstat1 < 3] = 0 std_tstat1[std_tstat1 < 3] = 0
fig = ortho(std2mm.data, mnivoxels, cmap=plt.cm.gray) fig = ortho(std2mm.data, mnivoxels, cmap=plt.cm.gray)
fig = ortho(std_tstat1, mnivoxels, cmap=plt.cm.inferno, fig=fig) fig = ortho(std_tstat1, mnivoxels, cmap=plt.cm.inferno, fig=fig)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
There are a few other useful functions tucked away in the There are a few other useful functions tucked away in the
[fsl.utils.image](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.image.html) [fsl.utils.image](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.image.html)
package, with more to be added in the future. The [`fsl.transform`]() package package, with more to be added in the future. The [`fsl.transform`]() package
also contains a wealth of functionality for working with linear (FLIRT) and also contains a wealth of functionality for working with linear (FLIRT) and
non-linear (FNIRT) transformations. non-linear (FNIRT) transformations.
<a class="anchor" id="fsl-wrapper-functions"></a> <a class="anchor" id="fsl-wrapper-functions"></a>
## FSL wrapper functions ## FSL wrapper functions
The The
[fsl.wrappers](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.wrappers.html) [fsl.wrappers](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.wrappers.html)
package is the home of "wrapper" functions for a range of FSL tools. You can package is the home of "wrapper" functions for a range of FSL tools. You can
use them to call an FSL tool from Python code, without having to worry about use them to call an FSL tool from Python code, without having to worry about
constructing a command-line, or saving/loading input/output images. constructing a command-line, or saving/loading input/output images.
> The `fsl.wrappers` functions also allow you to submit jobs to be run on the
> cluster - this is described [below](#submitting-to-the-cluster).
You can use the FSL wrapper functions with file names, similar to calling the You can use the FSL wrapper functions with file names, similar to calling the
corresponding tool via the command-line: corresponding tool via the command-line:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
from fsl.wrappers import bet, robustfov, LOAD from fsl.wrappers import bet, robustfov, LOAD
robustfov('08_fslpy/bighead', 'bighead_cropped') robustfov('08_fslpy/bighead', 'bighead_cropped')
render('08_fslpy/bighead bighead_cropped -cm blue') render('08_fslpy/bighead bighead_cropped -cm blue')
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
The `fsl.wrapper` functions strive to provide an interface which is as close The `fsl.wrappers` functions strive to provide an interface which is as close
as possible to the command-line tool - most functions use positional arguments as possible to the command-line tool - most functions use positional arguments
for required options, and keyword arguments for all other options, with for required options, and keyword arguments for all other options, with
argument names equivalent to command line option names. For example, the usage argument names equivalent to command line option names. For example, the usage
for the command-line `bet` tool is as follows: for the command-line `bet` tool is as follows:
> ``` > ```
> Usage: bet <input> <output> [options] > Usage: bet <input> <output> [options]
> >
> Main bet2 options: > Main bet2 options:
> -o generate brain surface outline overlaid onto original image > -o generate brain surface outline overlaid onto original image
> -m generate binary brain mask > -m generate binary brain mask
> -s generate approximate skull image > -s generate approximate skull image
> -n don't generate segmented brain image output > -n don't generate segmented brain image output
> -f <f> fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates > -f <f> fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates
> -g <g> vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top > -g <g> vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top
> -r <r> head radius (mm not voxels); initial surface sphere is set to half of this > -r <r> head radius (mm not voxels); initial surface sphere is set to half of this
> -c <x y z> centre-of-gravity (voxels not mm) of initial mesh surface. > -c <x y z> centre-of-gravity (voxels not mm) of initial mesh surface.
> ... > ...
> ``` > ```
So to use the `bet()` wrapper function, pass `<input>` and `<output>` as So to use the `bet()` wrapper function, pass `<input>` and `<output>` as
positional arguments, and pass the additional options as keyword arguments: positional arguments, and pass the additional options as keyword arguments:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
bet('bighead_cropped', 'bighead_cropped_brain', f=0.3, m=True, s=True) bet('bighead_cropped', 'bighead_cropped_brain', f=0.3, m=True, s=True)
render('bighead_cropped -b 40 ' render('bighead_cropped -b 40 '
'bighead_cropped_brain -cm hot ' 'bighead_cropped_brain -cm hot '
'bighead_cropped_brain_skull -ot mask -mc 0.4 0.4 1 ' 'bighead_cropped_brain_skull -ot mask -mc 0.4 0.4 1 '
'bighead_cropped_brain_mask -ot mask -mc 0 1 0 -o -w 5') 'bighead_cropped_brain_mask -ot mask -mc 0 1 0 -o -w 5')
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
> Some FSL commands accept arguments which cannot be used as Python > Some FSL commands accept arguments which cannot be used as Python
> identifiers - for example, the `-2D` option to `flirt` cannot be used as an > identifiers - for example, the `-2D` option to `flirt` cannot be used as an
> identifier in Python, because it begins with a number. In situations like > identifier in Python, because it begins with a number. In situations like
> this, an alias is used. So to set the `-2D` option to `flirt`, you can do this: > this, an alias is used. So to set the `-2D` option to `flirt`, you can do this:
> >
> ``` > ```
> # "twod" applies the -2D flag > # "twod" applies the -2D flag
> flirt('source.nii.gz', 'ref.nii.gz', omat='src2ref.mat', twod=True) > flirt('source.nii.gz', 'ref.nii.gz', omat='src2ref.mat', twod=True)
> ``` > ```
<a class="anchor" id="in-memory-images"></a> <a class="anchor" id="in-memory-images"></a>
### In-memory images ### In-memory images
It can be quite awkward to combine image processing with FSL tools and image It can be quite awkward to combine image processing with FSL tools and image
processing in Python. The `fsl.wrapper` package tries to make this a little processing in Python. The `fsl.wrappers` package tries to make this a little
easier for you - if you are working with image data in Python, you can pass easier for you - if you are working with image data in Python, you can pass
`Image` or `nibabel` objects directly into `fsl.wrapper` functions - they will `Image` or `nibabel` objects directly into `fsl.wrappers` functions - they will
be automatically saved to temporary files and passed to the underlying FSL be automatically saved to temporary files and passed to the underlying FSL
command: command:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
cropped = Image('bighead_cropped') cropped = Image('bighead_cropped')
bet(cropped, 'bighead_cropped_brain') bet(cropped, 'bighead_cropped_brain')
betted = Image('bighead_cropped_brain') betted = Image('bighead_cropped_brain')
fig = ortho(cropped.data, (80, 112, 85), cmap=plt.cm.gray) fig = ortho(cropped.data, (80, 112, 85), cmap=plt.cm.gray)
fig = ortho(betted .data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig) fig = ortho(betted .data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
<a class="anchor" id="loading-outputs-into-python"></a> <a class="anchor" id="loading-outputs-into-python"></a>
### Loading outputs into Python ### Loading outputs into Python
By using the special `fsl.wrappers.LOAD` symbol, you can have any output By using the special `fsl.wrappers.LOAD` symbol, you can also have any output
files produced by the tool automatically loaded in too: files produced by the tool automatically loaded:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
cropped = Image('bighead_cropped') cropped = Image('bighead_cropped')
betted = bet(cropped, LOAD)['output'] betted = bet(cropped, LOAD)['output']
fig = ortho(cropped.data, (80, 112, 85), cmap=plt.cm.gray) fig = ortho(cropped.data, (80, 112, 85), cmap=plt.cm.gray)
fig = ortho(betted .data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig) fig = ortho(betted .data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
You can use the `LOAD` symbol for any output argument - any output files which You can use the `LOAD` symbol for any output argument - any output files which
are loaded will be returned in a dictionary, with the argument name used as are loaded will be returned in a dictionary, with the argument name used as
the key: the key:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
from fsl.wrappers import flirt from fsl.wrappers import flirt
std2mm = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm'))) std2mm = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm')))
tstat1 = Image(op.join('08_fslpy', 'fmri.feat', 'stats', 'tstat1')) tstat1 = Image(op.join('08_fslpy', 'fmri.feat', 'stats', 'tstat1'))
func2std = np.loadtxt(op.join('08_fslpy', 'fmri.feat', 'reg', 'example_func2standard.mat')) func2std = np.loadtxt(op.join('08_fslpy', 'fmri.feat', 'reg', 'example_func2standard.mat'))
aligned = flirt(tstat1, std2mm, applyxfm=True, init=func2std, out=LOAD) aligned = flirt(tstat1, std2mm, applyxfm=True, init=func2std, out=LOAD)
print(aligned) print(aligned)
aligned = aligned['out'].data aligned = aligned['out'].data
aligned[aligned < 1] = 0 aligned[aligned < 1] = 0
fig = ortho(std2mm .data, (45, 54, 45), cmap=plt.cm.gray) fig = ortho(std2mm .data, (45, 54, 45), cmap=plt.cm.gray)
fig = ortho(aligned.data, (45, 54, 45), cmap=plt.cm.inferno, fig=fig) fig = ortho(aligned.data, (45, 54, 45), cmap=plt.cm.inferno, fig=fig)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
For tools like `bet`, which expect an output *prefix* or *basename*, you can For tools like `bet` and `fast`, which expect an output *prefix* or
just set the prefix to `LOAD` - all output files with that prefix will be *basename*, you can just set the prefix to `LOAD` - all output files with that
available in the returned dictionary: prefix will be available in the returned dictionary:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
img = Image('bighead_cropped') img = Image('bighead_cropped')
betted = bet(img, LOAD, f=0.3, m=True) betted = bet(img, LOAD, f=0.3, m=True)
print(betted) print(betted)
fig = ortho(img .data, (80, 112, 85), cmap=plt.cm.gray) fig = ortho(img .data, (80, 112, 85), cmap=plt.cm.gray)
fig = ortho(betted['output'] .data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig) fig = ortho(betted['output'] .data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig)
fig = ortho(betted['output_mask'].data, (80, 112, 85), cmap=plt.cm.summer, fig=fig, alpha=0.5) fig = ortho(betted['output_mask'].data, (80, 112, 85), cmap=plt.cm.summer, fig=fig, alpha=0.5)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
<a class="anchor" id="the-fslmaths-wrapper"></a> <a class="anchor" id="the-fslmaths-wrapper"></a>
### The `fslmaths` wrapper ### The `fslmaths` wrapper
*Most* of the `fsl.wrapper` functions aim to provide an interface which is as *Most* of the `fsl.wrappers` functions aim to provide an interface which is as
close as possible to the underlying FSL tool. Ideally, if you read the close as possible to the underlying FSL tool. Ideally, if you read the
command-line help for a tool, you should be able to figure out how to use the command-line help for a tool, you should be able to figure out how to use the
corresponding wrapper function. The wrapper for the `fslmaths` command is a corresponding wrapper function. The wrapper for the `fslmaths` command is a
little different, however. It provides more of an object-oriented interface, little different, however. It provides more of an object-oriented interface,
which is hopefully a little easier to use from within Python. which is hopefully a little easier to use from within Python.
You can apply an `fslmaths` operation by specifying the input file, *chaining* You can apply an `fslmaths` operation by specifying the input file, *chaining*
method calls together, and finally calling the `run()` method. For example: method calls together, and finally calling the `run()` method. For example:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
from fsl.wrappers import fslmaths from fsl.wrappers import fslmaths
fslmaths('bighead_cropped') \ fslmaths('bighead_cropped') \
.mas( 'bighead_cropped_brain_mask') \ .mas( 'bighead_cropped_brain_mask') \
.run( 'bighead_cropped_brain') .run( 'bighead_cropped_brain')
render('bighead_cropped bighead_cropped_brain -cm hot') render('bighead_cropped bighead_cropped_brain -cm hot')
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
Of course, you can also use the `fslmaths` wrapper with in-memory images: Of course, you can also use the `fslmaths` wrapper with in-memory images:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
wholehead = Image('bighead_cropped') wholehead = Image('bighead_cropped')
brainmask = Image('bighead_cropped_brain_mask') brainmask = Image('bighead_cropped_brain_mask')
eroded = fslmaths(brainmask).ero().ero().run() eroded = fslmaths(brainmask).ero().ero().run()
erodedbrain = fslmaths(wholehead).mas(eroded).run() erodedbrain = fslmaths(wholehead).mas(eroded).run()
fig = ortho(wholehead .data, (80, 112, 85), cmap=plt.cm.gray) fig = ortho(wholehead .data, (80, 112, 85), cmap=plt.cm.gray)
fig = ortho(brainmask .data, (80, 112, 85), cmap=plt.cm.summer, fig=fig) fig = ortho(brainmask .data, (80, 112, 85), cmap=plt.cm.summer, fig=fig)
fig = ortho(erodedbrain.data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig) fig = ortho(erodedbrain.data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig)
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
<a class="anchor" id="the-filetree"></a> <a class="anchor" id="the-filetree"></a>
## The `filetree` ## The `filetree`
todo
<a class="anchor" id="calling-shell-commands"></a> <a class="anchor" id="calling-shell-commands"></a>
## Calling shell commands ## Calling shell commands
The The
[`fsl.utils.run`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.run.html) [`fsl.utils.run`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.run.html)
module provides the `run` and `runfsl` functions, which are wrappers around module provides the `run` and `runfsl` functions, which are wrappers around
the built-in [`subprocess` the built-in [`subprocess`
library](https://docs.python.org/3/library/subprocess.html). library](https://docs.python.org/3/library/subprocess.html).
The default behaviour of `run` is to return the standard output of the The default behaviour of `run` is to return the standard output of the
command: command:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
from fsl.utils.run import run from fsl.utils.run import run
# You can pass the command # You can pass the command
# and its arguments as a single # and its arguments as a single
# string, or as a sequence # string, or as a sequence
print('Lines in this notebook:', run('wc -l 08_fslpy.md').strip()) print('Lines in this notebook:', run('wc -l 08_fslpy.md').strip())
print('Words in this notebook:', run(['wc', '-w', '08_fslpy.md']).strip()) print('Words in this notebook:', run(['wc', '-w', '08_fslpy.md']).strip())
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
But you can control what `run` returns, depending on your needs. Let's create But you can control what `run` returns, depending on your needs. Let's create
a little script to demonstrate the options: a little script to demonstrate the options:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
%%writefile mycmd %%writefile mycmd
#!/usr/bin/env bash #!/usr/bin/env bash
exitcode=$1 exitcode=$1
echo "Standard output!" echo "Standard output!"
echo "Standard error :(" >&2 echo "Standard error :(" >&2
exit $exitcode exit $exitcode
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
And let's not forget to make it executable: And let's not forget to make it executable:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
!chmod a+x mycmd !chmod a+x mycmd
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
You can use the `stdout`, `stderr` and `exitcode` arguments to control the You can use the `stdout`, `stderr` and `exitcode` arguments to control the
return value: return value:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
print('run("./mycmd 0"): ', print('run("./mycmd 0"): ',
run("./mycmd 0").strip()) run("./mycmd 0").strip())
print('run("./mycmd 0", stdout=False): ', print('run("./mycmd 0", stdout=False): ',
run("./mycmd 0", stdout=False)) run("./mycmd 0", stdout=False))
print('run("./mycmd 0", exitcode=True):', print('run("./mycmd 0", exitcode=True):',
run("./mycmd 0", exitcode=True)) run("./mycmd 0", exitcode=True))
print('run("./mycmd 0", stdout=False, exitcode=True):', print('run("./mycmd 0", stdout=False, exitcode=True):',
run("./mycmd 0", stdout=False, exitcode=True)) run("./mycmd 0", stdout=False, exitcode=True))
print('run("./mycmd 0", stderr=True): ', print('run("./mycmd 0", stderr=True): ',
run("./mycmd 0", stderr=True)) run("./mycmd 0", stderr=True))
print('run("./mycmd 0", stdout=False, stderr=True): ', print('run("./mycmd 0", stdout=False, stderr=True): ',
run("./mycmd 0", stdout=False, stderr=True).strip()) run("./mycmd 0", stdout=False, stderr=True).strip())
print('run("./mycmd 0", stderr=True, exitcode=True):', print('run("./mycmd 0", stderr=True, exitcode=True):',
run("./mycmd 0", stderr=True, exitcode=True)) run("./mycmd 0", stderr=True, exitcode=True))
print('run("./mycmd 1", exitcode=True):', print('run("./mycmd 1", exitcode=True):',
run("./mycmd 1", exitcode=True)) run("./mycmd 1", exitcode=True))
print('run("./mycmd 1", stdout=False, exitcode=True):', print('run("./mycmd 1", stdout=False, exitcode=True):',
run("./mycmd 1", stdout=False, exitcode=True)) run("./mycmd 1", stdout=False, exitcode=True))
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
So if only one of `stdout`, `stderr`, or `exitcode` is `True`, `run` will only So if only one of `stdout`, `stderr`, or `exitcode` is `True`, `run` will only
return the corresponding value. Otherwise `run` will return a tuple which return the corresponding value. Otherwise `run` will return a tuple which
contains the requested outputs. contains the requested outputs.
If you run a command which returns a non-0 exit code, the default behaviour If you run a command which returns a non-0 exit code, the default behaviour
(if you don't set `exitcode=True`) is for a `RuntimeError` to be raised: (if you don't set `exitcode=True`) is for a `RuntimeError` to be raised:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
run("./mycmd 99") run("./mycmd 99")
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
<a class="anchor" id="runfsl-and-submit"></a> <a class="anchor" id="the-runfsl-function"></a>
### `runfsl` and `submit` ### The `runfsl` function
The `runfsl` function is a wrapper around `run` which simply makes sure that The `runfsl` function is a wrapper around `run` which simply makes sure that
the command you are calling is inside the `$FSLDIR/bin/` directory. It has the the command you are calling is inside the `$FSLDIR/bin/` directory. It has the
same usage as the `run` function: same usage as the `run` function:
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` ```
from fsl.utils.run import runfsl from fsl.utils.run import runfsl
runfsl('fslroi 08_fslpy/bighead_cropped bighead_slices 0 -1 0 -1 90 5') runfsl('bet 08_fslpy/bighead_cropped bighead_cropped_brain')
runfsl('fslroi bighead_cropped_brain bighead_slices 0 -1 0 -1 90 3')
runfsl('fast -o bighead_fast bighead_slices') runfsl('fast -o bighead_fast bighead_slices')
render('-vl 80 112 91 -xh -yh '
'08_fslpy/bighead_cropped '
'bighead_slices.nii.gz -cm brain_colours_1hot -b 30 '
'bighead_fast_seg.nii.gz -ot label -o')
```
%% Cell type:markdown id: tags:
<a class="anchor" id="submitting-to-the-cluster"></a>
### Submitting to the cluster
Both the `run` and `runfsl` accept an argument called `submit`, which allows
you to submit jobs to be executed on the cluster via the FSL `fsl_sub`
command.