Commit 39738add authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

BF: typo

parent 59b1b7c7
......@@ -1487,7 +1487,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Once the job finishes, we shouldd be able to read the usual `.o` and `.e`\n",
"Once the job finishes, we should be able to read the usual `.o` and `.e`\n",
"files:"
]
},
......@@ -1550,9 +1550,9 @@
"metadata": {},
"source": [
"When you use `submit=True`, you can also specify cluster submission options -\n",
"you can include any arguments to the\n",
"you can include any arguments that are accepted by the\n",
"[`fslsub.submit`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.fslsub.html#fsl.utils.fslsub.submit)\n",
"function:"
"function"
]
},
{
......
%% Cell type:markdown id: tags:
# `fslpy`
**Important:** Portions of this practical require `fslpy` 2.9.0, due to be
released with FSL 6.0.4, in Spring 2020.
[`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
for working with FSL and with neuroimaging data from Python.
This practical highlights some of the most useful features provided by
`fslpy`. You may find `fslpy` useful if you are writing Python code to
perform analyses and image processing in conjunction with FSL.
> **Note**: `fslpy` is distinct from `fslpython` - `fslpython` is the Python
> environment that is baked into FSL. `fslpy` is a Python library which is
> installed into the `fslpython` environment.
* [The `Image` class, and other data types](#the-image-class-and-other-data-types)
* [Creating images](#creating-images)
* [Working with image data](#working-with-image-data)
* [Loading other file types](#loading-other-file-types)
* [NIfTI coordinate systems](#nifti-coordinate-systems)
* [Image processing](#image-processing)
* [FSL wrapper functions](#fsl-wrapper-functions)
* [In-memory images](#in-memory-images)
* [Loading outputs into Python](#loading-outputs-into-python)
* [The `fslmaths` wrapper](#the-fslmaths-wrapper)
* [The `FileTree`](#the-filetree)
* [Describing your data](#describing-your-data)
* [Using the `FileTree`](#using-the-filetree)
* [Building a processing pipeline with `FileTree`](#building-a-processing-pipeline-with-filetree)
* [The `FileTreeQuery`](#the-filetreequery)
* [Calling shell commands](#calling-shell-commands)
* [The `runfsl` function](#the-runfsl-function)
* [Submitting to the cluster](#submitting-to-the-cluster)
* [Redirecting output](#redirecting-output)
* [FSL atlases](#fsl-atlases)
* [Querying atlases](#querying-atlases)
* [Loading atlas images](#loading-atlas-images)
* [Working with atlases](#working-with-atlases)
Let's start with some standard imports and environment set-up:
%% Cell type:code id: tags:
```
%matplotlib inline
import matplotlib.pyplot as plt
import os
import os.path as op
import nibabel as nib
import numpy as np
import warnings
warnings.filterwarnings("ignore")
```
%% Cell type:markdown id: tags:
And a little function that we can use to generate a simple orthographic plot:
%% Cell type:code id: tags:
```
def ortho(data, voxel, fig=None, cursor=False, **kwargs):
"""Simple orthographic plot of a 3D array using matplotlib.
:arg data: 3D numpy array
:arg voxel: XYZ coordinates for each slice
:arg fig: Existing figure and axes for overlay plotting
:arg cursor: Show a cursor at the `voxel`
All other arguments are passed through to the `imshow` function.
:returns: The figure and orthogaxes (which can be passed back in as the
`fig` argument to plot overlays).
"""
data = np.asanyarray(data, dtype=np.float)
data[data <= 0] = np.nan
x, y, z = voxel
xslice = np.flipud(data[x, :, :].T)
yslice = np.flipud(data[:, y, :].T)
zslice = np.flipud(data[:, :, z].T)
if fig is None:
fig = plt.figure()
xax = fig.add_subplot(1, 3, 1)
yax = fig.add_subplot(1, 3, 2)
zax = fig.add_subplot(1, 3, 3)
else:
fig, xax, yax, zax = fig
xax.imshow(xslice, **kwargs)
yax.imshow(yslice, **kwargs)
zax.imshow(zslice, **kwargs)
if cursor:
cargs = {'color' : (0, 1, 0), 'linewidth' : 1}
xax.axvline( y, **cargs)
xax.axhline(data.shape[2] - z, **cargs)
yax.axvline( x, **cargs)
yax.axhline(data.shape[2] - z, **cargs)
zax.axvline( x, **cargs)
zax.axhline(data.shape[1] - y, **cargs)
for ax in (xax, yax, zax):
ax.set_xticks([])
ax.set_yticks([])
fig.tight_layout(pad=0)
return (fig, xax, yax, zax)
```
%% Cell type:markdown id: tags:
And another function which uses FSLeyes for more complex plots:
%% Cell type:code id: tags:
```
def render(cmdline):
import shlex
import IPython.display as display
prefix = '-of screenshot.png -hl -c 2 '
try:
from fsleyes.render import main
main(shlex.split(prefix + cmdline))
except ImportError:
# fall-back for macOS - we have to run
# FSLeyes render in a separate process
from fsl.utils.run import runfsl
prefix = 'render ' + prefix
runfsl(prefix + cmdline, env={})
return display.Image('screenshot.png')
```
%% Cell type:markdown id: tags:
<a class="anchor" id="the-image-class-and-other-data-types"></a>
## The `Image` class, and other data types
The
[`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
some handy functionality if you need to work with coordinate transformations,
or do some FSL-specific processing. The `Image` class provides features such
as:
- Support for NIFTI1, NIFTI2, and ANALYZE image files
- Access to affine transformations between the voxel, FSL and world coordinate
systems
- Ability to load metadata from BIDS sidecar files
Some simple image processing routines are also provided - these are covered
[below](#image-processing).
<a class="anchor" id="creating-images"></a>
### Creating images
It's easy to create an `Image` - you can create one from a file name:
%% Cell type:code id: tags:
```
from fsl.data.image import Image
stddir = op.expandvars('${FSLDIR}/data/standard/')
# load a FSL image - the file
# suffix is optional, just like
# in real FSL-land!
img = Image(op.join(stddir, 'MNI152_T1_1mm'))
print(img)
```
%% Cell type:markdown id: tags:
You can create an `Image` from an existing `nibabel` image:
%% Cell type:code id: tags:
```
# load a nibabel image, and
# convert it into an FSL image
nibimg = nib.load(op.join(stddir, 'MNI152_T1_1mm.nii.gz'))
img = Image(nibimg)
```
%% Cell type:markdown id: tags:
Or you can create an `Image` from a `numpy` array:
%% Cell type:code id: tags:
```
data = np.zeros((100, 100, 100))
img = Image(data, xform=np.eye(4))
```
%% Cell type:markdown id: tags:
You can save an image to file via the `save` method:
%% Cell type:code id: tags:
```
img.save('empty.nii.gz')
```
%% Cell type:markdown id: tags:
`Image` objects have all of the attributes you might expect:
%% Cell type:code id: tags:
```
stddir = op.expandvars('${FSLDIR}/data/standard/')
std1mm = Image(op.join(stddir, 'MNI152_T1_1mm'))
print('name: ', std1mm.name)
print('file: ', std1mm.dataSource)
print('NIfTI version:', std1mm.niftiVersion)
print('ndim: ', std1mm.ndim)
print('shape: ', std1mm.shape)
print('dtype: ', std1mm.dtype)
print('nvals: ', std1mm.nvals)
print('pixdim: ', std1mm.pixdim)
```
%% Cell type:markdown id: tags:
and a number of useful methods:
%% Cell type:code id: tags:
```
std2mm = Image(op.join(stddir, 'MNI152_T1_2mm'))
mask2mm = Image(op.join(stddir, 'MNI152_T1_2mm_brain_mask'))
print(std1mm.sameSpace(std2mm))
print(std2mm.sameSpace(mask2mm))
print(std2mm.getAffine('voxel', 'world'))
```
%% Cell type:markdown id: tags:
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`
attribute:
%% Cell type:code id: tags:
```
print(std2mm)
print(std2mm.nibImage)
```
%% Cell type:markdown id: tags:
<a class="anchor" id="working-with-image-data"></a>
### Working with image data
You can get the image data as a `numpy` array via the `data` attribute:
%% Cell type:code id: tags:
```
data = std2mm.data
print(data.min(), data.max())
ortho(data, (45, 54, 45))
```
%% Cell type:markdown id: tags:
> 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.
You can also read and write data directly via the `Image` object:
%% Cell type:code id: tags:
```
slc = std2mm[:, :, 45]
std2mm[0:10, :, :] *= 2
```
%% Cell type:markdown id: tags:
Doing so has some advantages that may or may not be useful, depending on your
use-case:
- 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
the `Image` to achieve this).
- The `Image` object will keep track of modifications to the data - this can
be queried via the `saveState` attribute.
<a class="anchor" id="loading-other-file-types"></a>
### Loading other file types
The
[`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
and neuroimaging data. Most of these are higher-level wrappers around the
corresponding `nibabel` types:
* The
[`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
convert it to a NIfTI image.
* The
[`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
directory<sup>*</sup>.
* The
[`fsl.data.mghimage.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
NIfTI images).
* The
[`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
FSL `dtifit` tool.
* The
[`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),
and
[`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
directories.
* Similarly, the
[`fsl.data.melodicanalysis`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.melodicanalysis.html)
and
[`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
directories.
* The
[`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),
and
[`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,
freesurfer, and ASCII VTK files respectively.
> <sup>*</sup>You must make sure that
> [`dcm2niix`](https://github.com/rordenlab/dcm2niix/) is installed on your
> system in order to use this class.
<a class="anchor" id="nifti-coordinate-systems"></a>
### NIfTI coordinate systems
The `Image.getAffine` method gives you access to affine transformations which
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
to voxels? Easy!
%% Cell type:code id: tags:
```
stddir = op.expandvars('${FSLDIR}/data/standard/')
std2mm = Image(op.join(stddir, 'MNI152_T1_2mm'))
mnicoords = np.array([[0, 0, 0],
[0, -18, 18]])
world2vox = std2mm.getAffine('world', 'voxel')
vox2world = std2mm.getAffine('voxel', 'world')
# Apply the world->voxel
# affine to the coordinates
voxcoords = (np.dot(world2vox[:3, :3], mnicoords.T)).T + world2vox[:3, 3]
# The code above is a bit fiddly, so
# instead of figuring it out, you can
# just use the transform() function:
from fsl.transform.affine import transform
voxcoords = transform(mnicoords, world2vox)
# just to double check, let's transform
# those voxel coordinates back into world
# coordinates
backtomni = transform(voxcoords, vox2world)
for m, v, b in zip(mnicoords, voxcoords, backtomni):
print(m, '->', v, '->', b)
```
%% Cell type:markdown id: tags:
> The `Image.getAffine` method can give you transformation matrices
> between any of these coordinate systems:
>
> - `'voxel'`: Image data voxel coordinates
> - `'world'`: mm coordinates, defined by the sform/qform of an image
> - `'fsl'`: The FSL coordinate system, used internally by many FSL tools
> (e.g. FLIRT)
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
coordinates of the voxel with peak activation.
> This is what people used to use `Featquery` for, back in the un-enlightened
> days.
Let's start by identifying the voxel with the biggest t-statistic:
%% Cell type:code id: tags:
```
featdir = op.join('08_fslpy', 'fmri.feat')
tstat1 = Image(op.join(featdir, 'stats', 'tstat1')).data
# Recall from the numpy practical that
# argmax gives us a 1D index into a
# flattened view of the array. We can
# use the unravel_index function to
# convert it into a 3D index.
peakvox = np.abs(tstat1).argmax()
peakvox = np.unravel_index(peakvox, tstat1.shape)
print('Peak voxel coordinates for tstat1:', peakvox, tstat1[peakvox])
```
%% Cell type:markdown id: tags:
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
directly from functional to standard space, in the `reg` directory:
%% Cell type:code id: tags:
```
func2std = np.loadtxt(op.join(featdir, 'reg', 'example_func2standard.mat'))
```
%% Cell type:markdown id: tags:
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
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.
Let's start by loading our functional image, and the MNI152 template (the
source and reference images of our FLIRT matrix):
%% Cell type:code id: tags:
```
func = Image(op.join(featdir, 'reg', 'example_func'))
std = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm')))
```
%% Cell type:markdown id: tags:
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,
which transforms our functional-space voxels into MNI world coordinates via:
1. functional voxels -> FLIRT source space
2. FLIRT source space -> FLIRT reference space
3. FLIRT referece space -> MNI world coordinates
%% Cell type:code id: tags:
```
vox2fsl = func.getAffine('voxel', 'fsl')
fsl2mni = std .getAffine('fsl', 'world')
```
%% Cell type:markdown id: tags:
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:
%% Cell type:code id: tags:
```
from fsl.transform.affine import concat
# To combine affines together, we
# have to list them in reverse -
# linear algebra is *weird*.
funcvox2mni = concat(fsl2mni, func2std, vox2fsl)
```
%% Cell type:markdown id: tags:
> Below we will use the
> [`fsl.transform.flirt.fromFlirt`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.transform.flirt.html#fsl.transform.flirt.fromFlirt)
> function, which does all of the above for us.
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:
%% Cell type:code id: tags:
```
mnicoords = transform(peakvox, funcvox2mni)
mnivoxels = transform(mnicoords, std.getAffine('world', 'voxel'))
mnivoxels = [int(round(v)) for v in mnivoxels]
print('Peak activation (MNI coordinates):', mnicoords)
print('Peak activation (MNI voxels): ', mnivoxels)
```
%% Cell type:markdown id: tags:
> 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
> structural-to-standard transformation too. But this is left as [an exercise
> for the
> reader](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.transform.fnirt.html).
<a class="anchor" id="image-processing"></a>
### Image processing
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
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
overlay it on the MNI template. This can be done using some handy functions
from the
[`fsl.utils.image.resample`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.image.resample.html)
module:
%% Cell type:code id: tags:
```
from fsl.transform.flirt import fromFlirt
from fsl.utils.image.resample import resampleToReference
featdir = op.join(op.join('08_fslpy', 'fmri.feat'))
tstat1 = Image(op.join(featdir, 'stats', 'tstat1'))
std = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm')))
# Load the func2standard FLIRT matrix, and adjust it
# so that it transforms from functional *world*
# coordinates into standard *world* coordinates -
# this is what is expected by the resampleToReference
# function, used below
func2std = np.loadtxt(op.join(featdir, 'reg', 'example_func2standard.mat'))
func2std = fromFlirt(func2std, tstat1, std, 'world', 'world')
# All of the functions in the resample module
# return a numpy array containing the resampled
# data, and an adjusted voxel-to-world affine
# transformation. But when using the
# resampleToReference function, the affine will
# be the same as the MNI152 2mm affine, so we
# can ignore it.
std_tstat1 = resampleToReference(tstat1, std, func2std)[0]
std_tstat1 = Image(std_tstat1, header=std.header)
```
%% Cell type:markdown id: tags:
Now that we have our t-statistic image in MNI152 space, we can plot it in
standard space using `matplotlib`:
%% Cell type:code id: tags:
```
stddir = op.expandvars('${FSLDIR}/data/standard/')
std2mm = Image(op.join(stddir, 'MNI152_T1_2mm'))
std_tstat1 = std_tstat1.data
std_tstat1[std_tstat1 < 3] = 0
fig = ortho(std2mm.data, mnivoxels, cmap=plt.cm.gray)
fig = ortho(std_tstat1, mnivoxels, cmap=plt.cm.inferno, fig=fig, cursor=True)
```
%% Cell type:markdown id: tags:
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)
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
non-linear (FNIRT) transformations.
<a class="anchor" id="fsl-wrapper-functions"></a>
## FSL wrapper functions
The
[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
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.
> 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
corresponding tool via the command-line:
%% Cell type:code id: tags:
```
from fsl.wrappers import bet, robustfov, LOAD
robustfov('08_fslpy/bighead', 'bighead_cropped')
render('08_fslpy/bighead bighead_cropped -cm blue')
```
%% Cell type:markdown id: tags:
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
for required options, and keyword arguments for all other options, with
argument names equivalent to command line option names. For example, the usage
for the command-line `bet` tool is as follows:
> ```
> Usage: bet <input> <output> [options]
>
> Main bet2 options:
> -o generate brain surface outline overlaid onto original image
> -m generate binary brain mask
> -s generate approximate skull image
> -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
> -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
> -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
positional arguments, and pass the additional options as keyword arguments:
%% Cell type:code id: tags:
```
bet('bighead_cropped', 'bighead_cropped_brain', f=0.3, m=True, s=True)
render('bighead_cropped -b 40 '
'bighead_cropped_brain -cm hot '
'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')
```
%% Cell type:markdown id: tags:
> Some FSL commands accept arguments which cannot be used as Python
> 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
> this, an alias is used. So to set the `-2D` option to `flirt`, you can do this:
>
> ```
> # "twod" applies the -2D flag
> flirt('source.nii.gz', 'ref.nii.gz', omat='src2ref.mat', twod=True)
> ```
>
> Some of the `fsl.wrappers` functions also support aliases which may make
> your code more readable. For example, when calling `bet`, you can use either
> `m=True` or `mask=True` to apply the `-m` command line flag.
<a class="anchor" id="in-memory-images"></a>
### In-memory images
It can be quite awkward to combine image processing with FSL tools and image
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
`Image` or `nibabel` objects directly into `fsl.wrappers` functions - they will
be automatically saved to temporary files and passed to the underlying FSL
command:
%% Cell type:code id: tags:
```
cropped = Image('bighead_cropped')
bet(cropped, 'bighead_cropped_brain')
betted = Image('bighead_cropped_brain')
fig = ortho(cropped.data, (80, 112, 85), cmap=plt.cm.gray)
fig = ortho(betted .data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig)
```
%% Cell type:markdown id: tags:
<a class="anchor" id="loading-outputs-into-python"></a>
### Loading outputs into Python
By using the special `fsl.wrappers.LOAD` symbol, you can also have any output
files produced by the tool automatically loaded into memory for you:
%% Cell type:code id: tags:
```
cropped = Image('bighead_cropped')
# The loaded result is called "output",
# because that is the name of the
# argument in the bet wrapper function.
betted = bet(cropped, LOAD).output
fig = ortho(cropped.data, (80, 112, 85), cmap=plt.cm.gray)
fig = ortho(betted .data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig)
```
%% Cell type:markdown id: tags:
You can use the `LOAD` symbol for any output argument - any output files which
are loaded will be available through the return value of the wrapper function:
%% Cell type:code id: tags:
```
from fsl.wrappers import flirt
std2mm = Image(op.expandvars(op.join('$FSLDIR', 'data', 'standard', 'MNI152_T1_2mm')))
tstat1 = Image(op.join('08_fslpy', 'fmri.feat', 'stats', 'tstat1'))
func2std = np.loadtxt(op.join('08_fslpy', 'fmri.feat', 'reg', 'example_func2standard.mat'))
aligned = flirt(tstat1, std2mm, applyxfm=True, init=func2std, out=LOAD)
# Here the resampled tstat image
# is called "out", because that
# is the name of the flirt argument.
aligned = aligned.out.data
aligned[aligned < 1] = 0
peakvox = np.abs(aligned).argmax()
peakvox = np.unravel_index(peakvox, aligned.shape)
fig = ortho(std2mm .data, peakvox, cmap=plt.cm.gray)
fig = ortho(aligned.data, peakvox, cmap=plt.cm.inferno, fig=fig, cursor=True)
```
%% Cell type:markdown id: tags:
For tools like `bet` and `fast`, which expect an output *prefix* or
*basename*, you can just set the prefix to `LOAD` - all output files with that
prefix will be available in the object that is returned:
%% Cell type:code id: tags:
```
img = Image('bighead_cropped')
betted = bet(img, LOAD, f=0.3, mask=True)
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_mask.data, (80, 112, 85), cmap=plt.cm.summer, fig=fig, alpha=0.5)
```
%% Cell type:markdown id: tags:
<a class="anchor" id="the-fslmaths-wrapper"></a>
### The `fslmaths` wrapper
*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
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
little different, however. It provides more of an object-oriented interface,
which is hopefully a little easier to use from within Python.
You can apply an `fslmaths` operation by specifying the input image,
*chaining* method calls together, and finally calling the `run()` method. For
example:
%% Cell type:code id: tags:
```
from fsl.wrappers import fslmaths
fslmaths('bighead_cropped') \
.mas( 'bighead_cropped_brain_mask') \
.run( 'bighead_cropped_brain')
render('bighead_cropped bighead_cropped_brain -cm hot')
```
%% Cell type:markdown id: tags:
Of course, you can also use the `fslmaths` wrapper with in-memory images:
%% Cell type:code id: tags:
```
wholehead = Image('bighead_cropped')
brainmask = Image('bighead_cropped_brain_mask')
eroded = fslmaths(brainmask).ero().ero().run()
erodedbrain = fslmaths(wholehead).mas(eroded).run()
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(erodedbrain.data, (80, 112, 85), cmap=plt.cm.inferno, fig=fig)
```
%% Cell type:markdown id: tags:
<a class="anchor" id="the-filetree"></a>
## The `FileTree`
The
[`fsl.utils.filetree`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.filetree.html)
library provides functionality which allows you to work with *structured data
directories*, such as HCP or BIDS datasets. You can use `filetree` for both
reading and for creating datasets.
This practical gives a very brief introduction to the `filetree` library -
refer to the [full
documentation](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.filetree.html)
to get a feel for how powerful it can be.
<a class="anchor" id="describing-your-data"></a>
### Describing your data
To introduce `filetree`, we'll begin with a small example. Imagine that we
have a dataset which looks like this:
> ```
> mydata
> ├── sub_A
> │   ├── ses_1
> │   │   └── T1w.nii.gz
> │   ├── ses_2
> │   │   └── T1w.nii.gz
> │   └── T2w.nii.gz
> ├── sub_B
> │   ├── ses_1
> │   │   └── T1w.nii.gz
> │   ├── ses_2
> │   │   └── T1w.nii.gz
> │   └── T2w.nii.gz
> └── sub_C
> ├── ses_1
> │   └── T1w.nii.gz
> ├── ses_2
> │   └── T1w.nii.gz
> └── T2w.nii.gz
> ```
(Run the code cell below to create a dummy data set with the above structure):
%% Cell type:code id: tags:
```
%%bash
for sub in A B C; do
subdir=mydata/sub_$sub/
mkdir -p $subdir
cp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz $subdir/T2w.nii.gz
for ses in 1 2; do
sesdir=$subdir/ses_$ses/
mkdir $sesdir
cp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz $sesdir/T1w.nii.gz
done
done
```
%% Cell type:markdown id: tags:
To use `filetree` with this dataset, we must first describe its structure - we
do this by creating a `.tree` file:
%% Cell type:code id: tags:
```
%%writefile mydata.tree
sub_{subject}
T2w.nii.gz
ses_{session}
T1w.nii.gz
```
%% Cell type:markdown id: tags:
A `.tree` file is simply a description of the structure of your data
directory - it describes the *file types* (also known as *templates*) which
are present in the dataset (`T1w` and `T2w`), and the *variables* which are
implicitly present in the structure of the dataset (`subject` and `session`).
<a class="anchor" id="using-the-filetree"></a>
### Using the `FileTree`
Now that we have a `.tree` file which describe our data, we can create a
`FileTree` to work with it:
%% Cell type:code id: tags:
```
from fsl.utils.filetree import FileTree
# Create a FileTree, giving
# it our tree specification,
# and the path to our data.
tree = FileTree.read('mydata.tree', 'mydata')
```
%% Cell type:markdown id: tags:
We can list all of the T1 images via the `FileTree.get_all` method. The
`glob_vars='all'` option tells the `FileTree` to fill in the `T1w` template
with all possible combinations of variables. The `FileTree.extract_variables`
method accepts a file path, and gives you back the variable values contained
within:
%% Cell type:code id: tags:
```
for t1file in tree.get_all('T1w', glob_vars='all'):
fvars = tree.extract_variables('T1w', t1file)
print(t1file, fvars)
```
%% Cell type:markdown id: tags:
The `FileTree.update` method allows you to "fill in" variable values; it
returns a new `FileTree` object which can be used on a selection of the
data set:
%% Cell type:code id: tags:
```
treeA = tree.update(subject='A')
for t1file in treeA.get_all('T1w', glob_vars='all'):
fvars = treeA.extract_variables('T1w', t1file)
print(t1file, fvars)
```
%% Cell type:markdown id: tags:
<a class="anchor" id="building-a-processing-pipeline-with-filetree"></a>
### Building a processing pipeline with `FileTree`
Let's say we want to run BET on all of our T1 images. Let's start by modifying
our `.tree` definition to include the BET outputs:
%% Cell type:code id: tags:
```
%%writefile mydata.tree
sub_{subject}
T2w.nii.gz
ses_{session}
T1w.nii.gz
T1w_brain.nii.gz
T1w_brain_mask.nii.gz
```
%% Cell type:markdown id: tags:
Now we can use the `FileTree` to generate the relevant file names for us,
which we can then pass on to BET. Here we'll use the `FileTree.get_all_trees`
method to create a sub-tree for each subject and each session:
%% Cell type:code id: tags:
```
from fsl.wrappers import bet
tree = FileTree.read('mydata.tree', 'mydata')
for subtree in tree.get_all_trees('T1w', glob_vars='all'):
t1file = subtree.get('T1w')
t1brain = subtree.get('T1w_brain')
print('Running BET: {} -> {} ...'.format(t1file, t1brain))
bet(t1file, t1brain, mask=True)
print('Done!')
example = tree.update(subject='A', session='1')
render('{} {} -ot mask -o -w 2 -mc 0 1 0'.format(
example.get('T1w'),
example.get('T1w_brain_mask')))
```
%% Cell type:markdown id: tags:
<a class="anchor" id="the-filetreequery"></a>
### The `FileTreeQuery`
The `filetree` module contains another class called the
[`FileTreeQuery`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.filetree.query.html),
which provides an interface that is more convenient if you are reading data
from large datasets with many different file types and variables.
When you create a `FileTreeQuery`, it scans the entire data directory and
identifies all of the values that are present for each variable defined in the
`.tree` file:
%% Cell type:code id: tags:
```
from fsl.utils.filetree import FileTreeQuery
tree = FileTree.read('mydata.tree', 'mydata')
query = FileTreeQuery(tree)
print('T1w variables:', query.variables('T1w'))
print('T2w variables:', query.variables('T2w'))
```
%% Cell type:markdown id: tags:
The `FileTreeQuery.query` method will return the paths to all existing files
which match a set of variable values:
%% Cell type:code id: tags:
```
print('All files for subject A')
for template in query.templates:
print(' {} files:'.format(template))
for match in query.query(template, subject='A'):
print(' ', match.filename)
```
%% Cell type:markdown id: tags:
<a class="anchor" id="calling-shell-commands"></a>
## Calling shell commands
The
[`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
the built-in [`subprocess`
library](https://docs.python.org/3/library/subprocess.html).
The default behaviour of `run` is to return the standard output of the
command:
%% Cell type:code id: tags:
```
from fsl.utils.run import run
# You can pass the command
# and its arguments as a single
# string, or as a sequence
print('Lines in this notebook:', run('wc -l 08_fslpy.md').strip())
print('Words in this notebook:', run(['wc', '-w', '08_fslpy.md']).strip())
```
%% Cell type:markdown id: tags:
But you can control what `run` returns, depending on your needs. Let's create
a little script to demonstrate the options:
%% Cell type:code id: tags:
```
%%writefile mycmd
#!/usr/bin/env bash
exitcode=$1
echo "Standard output!"
echo "Standard error :(" >&2
exit $exitcode
```
%% Cell type:markdown id: tags:
And let's not forget to make it executable:
%% Cell type:code id: tags:
```
!chmod a+x mycmd
```
%% Cell type:markdown id: tags:
You can use the `stdout`, `stderr` and `exitcode` arguments to control the
return value:
%% Cell type:code id: tags:
```
print('run("./mycmd 0"): ',
run("./mycmd 0").strip())
print('run("./mycmd 0", stdout=False): ',
run("./mycmd 0", stdout=False))
print('run("./mycmd 0", exitcode=True):',
run("./mycmd 0", exitcode=True))
print('run("./mycmd 0", stdout=False, exitcode=True):',
run("./mycmd 0", stdout=False, exitcode=True))
print('run("./mycmd 0", stderr=True): ',
run("./mycmd 0", stderr=True))
print('run("./mycmd 0", stdout=False, stderr=True): ',
run("./mycmd 0", stdout=False, stderr=True).strip())
print('run("./mycmd 0", stderr=True, exitcode=True):',
run("./mycmd 0", stderr=True, exitcode=True))
print('run("./mycmd 1", exitcode=True):',
run("./mycmd 1", exitcode=True))
print('run("./mycmd 1", stdout=False, exitcode=True):',
run("./mycmd 1", stdout=False, exitcode=True))
```
%% Cell type:markdown id: tags:
So if only one of `stdout`, `stderr`, or `exitcode` is `True`, `run` will only
return the corresponding value. Otherwise `run` will return a tuple which
contains the requested outputs.
If you run a command which returns a non-0 exit code, the default behaviour
(if you don't set `exitcode=True`) is for a `RuntimeError` to be raised:
%% Cell type:code id: tags:
```
run("./mycmd 99")
```
%% Cell type:markdown id: tags:
<a class="anchor" id="the-runfsl-function"></a>
### The `runfsl` function
The `runfsl` function is a wrapper around `run` which simply makes sure that
the command you are calling is inside the `$FSLDIR/bin/` directory. It has the
same usage as the `run` function:
%% Cell type:code id: tags:
```
from fsl.utils.run import runfsl
runfsl('bet 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')
render('-vl 80 112 91 -xh -yh '
'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.
> Cluster submission is handled by the
> [`fsl.utils.fslsub`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.fslsub.html)
> module - it contains lower level functions for managing and querying jobs
> that have been submitted to the cluster. The functions defined in this
> module can be used directly if you have more complicated requirements.
The semantics of the `run` and `runfsl` functions are slightly different when
you use the `submit` option - when you submit a job, the `run`/`runfsl`
functions will return immediately, and will return a string containing the job
ID:
%% Cell type:code id: tags:
```
jobid = run('ls', submit=True)
print('Job ID:', jobid)
```
%% Cell type:markdown id: tags:
Once the job finishes, we shouldd be able to read the usual `.o` and `.e`
Once the job finishes, we should be able to read the usual `.o` and `.e`
files:
%% Cell type:code id: tags:
```
stdout = f'ls.o{jobid}'
print('Job output')
print(open(stdout).read())
```
%% Cell type:markdown id: tags:
All of the `fsl.wrappers` functions also accept the `submit` argument:
%% Cell type:code id: tags:
```
jobid = bet('08_fslpy/bighead', 'bighead_brain', submit=True)
print('Job ID:', jobid)
```
%% Cell type:markdown id: tags:
> But an error will occur if you try to pass in-memory images, or `LOAD` any
> outputs when you call a wrapper function with `submit=True`.
After submitting a job, you can use the `wait` function to wait until a job
has completed:
%% Cell type:code id: tags:
```
from fsl.utils.run import wait
jobid = bet('08_fslpy/bighead', 'bighead_brain', submit=True)
print('Job ID:', jobid)
wait(jobid)
print('Done!')
render('08_fslpy/bighead bighead_brain -cm hot')
```
%% Cell type:markdown id: tags:
When you use `submit=True`, you can also specify cluster submission options -
you can include any arguments to the
you can include any arguments that are accepted by the
[`fslsub.submit`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.fslsub.html#fsl.utils.fslsub.submit)
function:
function
%% Cell type:code id: tags:
```
jobs = []
jobs.append(runfsl('robustfov -i 08_fslpy/bighead -r bighead_cropped', submit=True, queue='short.q'))
jobs.append(runfsl('bet bighead_cropped bighead_brain', submit=True, queue='short.q', wait_for=jobs[-1]))
jobs.append(runfsl('fslroi bighead_brain bighead_slices 0 -1 111 3 0 -1', submit=True, queue='short.q', wait_for=jobs[-1]))
jobs.append(runfsl('fast -o bighead_fast bighead_slices', submit=True, queue='short.q', wait_for=jobs[-1]))
print('Waiting for', jobs, '...')
wait(jobs)
render('-vl 80 112 91 -xh -zh -hc '
'bighead_brain '
'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="redirecting-output"></a>
### Redirecting output
The `log` option, accepted by both `run` and `fslrun`, allows for more
fine-grained control over what is done with the standard output and error
streams.
You can use `'tee'` to redirect the standard output and error streams of the
command to the standard output and error streams of the calling command (your
python script):
%% Cell type:code id: tags:
```
print('Teeing:')
_ = run('./mycmd 0', log={'tee' : True})
```
%% Cell type:markdown id: tags:
Or you can use `'stdout'` and `'stderr'` to redirect the standard output and
error streams of the command to files:
%% Cell type:code id: tags:
```
with open('stdout.log', 'wt') as o, \
open('stderr.log', 'wt') as e:
run('./mycmd 0', log={'stdout' : o, 'stderr' : e})
print('\nRedirected stdout:')
!cat stdout.log
print('\nRedirected stderr:')
!cat stderr.log
```
%% Cell type:markdown id: tags:
Finally, you can use `'cmd'` to log the command itself to a file (useful for
pipeline logging):
%% Cell type:code id: tags:
```
with open('commands.log', 'wt') as cmdlog:
run('./mycmd 0', log={'cmd' : cmdlog})
run('wc -l 08_fslpy.md', log={'cmd' : cmdlog})
print('\nCommand log:')
!cat commands.log
```
%% Cell type:markdown id: tags:
<a class="anchor" id="fsl-atlases"></a>
## FSL atlases
The
[`fsl.data.atlases`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.data.atlases.html)
module provides access to all of the atlas images that are stored in the
`$FSLDIR/data/atlases/` directory of a standard FSL installation. It can be
used to load and query probabilistic and label-based atlases.
The `atlases` module needs to be initialised using the `rescanAtlases` function:
%% Cell type:code id: tags:
```
import fsl.data.atlases as atlases
atlases.rescanAtlases()
```
%% Cell type:markdown id: tags:
<a class="anchor" id="querying-atlases"></a>
### Querying atlases
You can list all of the available atlases using `listAtlases`:
%% Cell type:code id: tags:
```
for desc in atlases.listAtlases():
print(desc)
```
%% Cell type:markdown id: tags:
`listAtlases` returns a list of `AtlasDescription` objects, each of which
contains descriptive information about one atlas. You can retrieve the
`AtlasDescription` for a specific atlas via the `getAtlasDescription`
function:
%% Cell type:code id: tags:
```
desc = atlases.getAtlasDescription('harvardoxford-cortical')
print(desc.name)
print(desc.atlasID)
print(desc.specPath)
print(desc.atlasType)
```
%% Cell type:markdown id: tags:
Each `AtlasDescription` maintains a list of `AtlasLabel` objects, each of
which represents one region that is defined in the atlas. You can access all
of the `AtlasLabel` objects via the `labels` attribute:
%% Cell type:code id: tags:
```
for lbl in desc.labels[:5]:
print(lbl)
```
%% Cell type:markdown id: tags:
Or you can retrieve a specific label using the `find` method:
%% Cell type:code id: tags:
```
# search by region name
print(desc.find(name='Occipital Pole'))
# or by label value
print(desc.find(value=48))
```
%% Cell type:markdown id: tags:
<a class="anchor" id="loading-atlas-images"></a>
### Loading atlas images
The `loadAtlas` function can be used to load the atlas image:
%% Cell type:code id: tags:
```
# For probabilistic atlases, you
# can ask for the 3D ROI image
# by setting loadSummary=True.
# You can also request a
# resolution - by default the
# highest resolution version
# will be loaded.
lblatlas = atlases.loadAtlas('harvardoxford-cortical',
loadSummary=True,
resolution=2)
# By default you will get the 4D
# probabilistic atlas image (for
# atlases for which this is
# available).
probatlas = atlases.loadAtlas('harvardoxford-cortical',
resolution=2)
print(lblatlas)
print(probatlas)
```
%% Cell type:markdown id: tags:
<a class="anchor" id="working-with-atlases"></a>
### Working with atlases
Both `LabelAtlas` and `ProbabilisticAtlas` objects have a method called `get`,
which can be used to extract ROI images for a specific region:
%% Cell type:code id: tags:
```
stddir = op.expandvars('${FSLDIR}/data/standard/')
std2mm = Image(op.join(stddir, 'MNI152_T1_2mm'))
frontal = lblatlas.get(name='Frontal Pole').data
frontal = np.ma.masked_where(frontal < 1, frontal)
fig = ortho(std2mm.data, (45, 54, 45), cmap=plt.cm.gray)
fig = ortho(frontal, (45, 54, 45), cmap=plt.cm.winter, fig=fig)
```
%% Cell type:markdown id: tags:
Calling `get` on a `ProbabilisticAtlas` will return a probability image:
%% Cell type:code id: tags:
```
stddir = op.expandvars('${FSLDIR}/data/standard/')
std2mm = Image(op.join(stddir, 'MNI152_T1_2mm'))
frontal = probatlas.get(name='Frontal Pole').data
frontal = np.ma.masked_where(frontal < 1, frontal)
fig = ortho(std2mm.data, (45, 54, 45), cmap=plt.cm.gray)
fig = ortho(frontal, (45, 54, 45), cmap=plt.cm.inferno, fig=fig)
```
%% Cell type:markdown id: tags:
The `get` method can be used to retrieve an image for a region by:
- an `AtlasLabel` object
- The region index
- The region value
- The region name
`LabelAtlas` objects have a method called `label`, which can be used to
interrogate the atlas at specific locations:
%% Cell type:code id: tags:
```
# The label method accepts 3D
# voxel or world coordinates
val = lblatlas.label((25, 52, 43), voxel=True)
lbl = lblatlas.find(value=val)
print('Region at voxel [25, 52, 43]: {} [{}]'.format(val, lbl.name))
# or a 3D weighted or binary mask
mask = np.zeros(lblatlas.shape)
mask[30:60, 30:60, 30:60] = 1
mask = Image(mask, header=lblatlas.header)
lbls, props = lblatlas.label(mask)
print('Labels in mask:')
for lbl, prop in zip(lbls, props):
lblname = lblatlas.find(value=lbl).name
print(' {} [{}]: {:0.2f}%'.format(lbl, lblname, prop))
```
%% Cell type:markdown id: tags:
`ProbabilisticAtlas` objects have an analogous method called `values`:
%% Cell type:code id: tags:
```
vals = probatlas.values((25, 52, 43), voxel=True)
print('Regions at voxel [25, 52, 43]:')
for idx, val in enumerate(vals):
if val > 0:
lbl = probatlas.find(index=idx)
print(' {} [{}]: {:0.2f}%'.format(lbl.value, lbl.name, val))
print('Average proportions of regions within mask:')
vals = probatlas.values(mask)
for idx, val in enumerate(vals):
if val > 0:
lbl = probatlas.find(index=idx)
print(' {} [{}]: {:0.2f}%'.format(lbl.value, lbl.name, val))
```
......
......@@ -1119,7 +1119,7 @@ print('Job ID:', jobid)
```
Once the job finishes, we shouldd be able to read the usual `.o` and `.e`
Once the job finishes, we should be able to read the usual `.o` and `.e`
files:
......@@ -1158,9 +1158,9 @@ render('08_fslpy/bighead bighead_brain -cm hot')
When you use `submit=True`, you can also specify cluster submission options -
you can include any arguments to the
you can include any arguments that are accepted by the
[`fslsub.submit`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.fslsub.html#fsl.utils.fslsub.submit)
function:
function
```
......
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