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[DOC] update FSL preprocess #1881

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Merged
merged 4 commits into from
Mar 16, 2017
Merged

[DOC] update FSL preprocess #1881

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9e4a94d
add documentation & doc tests to fsl preprocess
neuroumbrage Feb 25, 2017
9c3f5ee
Merge remote-tracking branch 'nipy/master'
neuroumbrage Mar 14, 2017
eb24c4d
fix accidental re-add
neuroumbrage Mar 14, 2017
f5f1b22
Fixed documentation
neuroumbrage Mar 14, 2017
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49 changes: 30 additions & 19 deletions nipype/interfaces/fsl/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -118,15 +118,17 @@ class BET(FSLCommand):
"""Use FSL BET command for skull stripping.

For complete details, see the `BET Documentation.
<http://www.fmrib.ox.ac.uk/fsl/bet2/index.html>`_
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide>`_

Examples
--------
>>> from nipype.interfaces import fsl
>>> from nipype.testing import example_data
>>> btr = fsl.BET()
>>> btr.inputs.in_file = example_data('structural.nii')
>>> btr.inputs.in_file = 'structural.nii'
>>> btr.inputs.frac = 0.7
>>> btr.inputs.out_file = 'brain_anat.nii'
>>> btr.cmdline # doctest: +ALLOW_UNICODE
'bet structural.nii brain_anat.nii -f 0.70'
>>> res = btr.run() # doctest: +SKIP

"""
Expand Down Expand Up @@ -275,7 +277,7 @@ class FASTOutputSpec(TraitedSpec):

mixeltype = File(desc="path/name of mixeltype volume file _mixeltype")

partial_volume_map = File(desc="path/name of partial volume file _pveseg")
partial_volume_map = File(desc='path/name of partial volume file _pveseg')
partial_volume_files = OutputMultiPath(File(
desc='path/name of partial volumes files one for each class, _pve_x'))

Expand All @@ -288,18 +290,17 @@ class FAST(FSLCommand):
""" Use FSL FAST for segmenting and bias correction.

For complete details, see the `FAST Documentation.
<http://www.fmrib.ox.ac.uk/fsl/fast4/index.html>`_
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST>`_

Examples
--------
>>> from nipype.interfaces import fsl
>>> from nipype.testing import example_data

Assign options through the ``inputs`` attribute:

>>> fastr = fsl.FAST()
>>> fastr.inputs.in_files = example_data('structural.nii')
>>> out = fastr.run() #doctest: +SKIP
>>> fastr.inputs.in_files = 'structural.nii'
>>> fastr.inputs.out_basename = 'fast_'
>>> fastr.cmdline # doctest: +ALLOW_UNICODE
'fast -o fast_ -S 1 structural.nii'
>>> out = fastr.run() # doctest: +SKIP

"""
_cmd = 'fast'
Expand All @@ -308,12 +309,12 @@ class FAST(FSLCommand):

def _format_arg(self, name, spec, value):
# first do what should be done in general
formated = super(FAST, self)._format_arg(name, spec, value)
formatted = super(FAST, self)._format_arg(name, spec, value)
if name == 'in_files':
# FAST needs the -S parameter value to correspond to the number
# of input images, otherwise it will ignore all but the first
formated = "-S %d %s" % (len(value), formated)
return formated
formatted = "-S %d %s" % (len(value), formatted)
return formatted

def _list_outputs(self):
outputs = self.output_spec().get()
Expand Down Expand Up @@ -526,7 +527,7 @@ class FLIRT(FSLCommand):
"""Use FSL FLIRT for coregistration.

For complete details, see the `FLIRT Documentation.
<http://www.fmrib.ox.ac.uk/fsl/flirt/index.html>`_
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT>`_

To print out the command line help, use:
fsl.FLIRT().inputs_help()
Expand Down Expand Up @@ -655,14 +656,18 @@ class MCFLIRT(FSLCommand):
"""Use FSL MCFLIRT to do within-modality motion correction.

For complete details, see the `MCFLIRT Documentation.
<http://www.fmrib.ox.ac.uk/fsl/mcflirt/index.html>`_
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT>`_

Examples
--------
>>> from nipype.interfaces import fsl
>>> from nipype.testing import example_data
>>> mcflt = fsl.MCFLIRT(in_file=example_data('functional.nii'), cost='mutualinfo')
>>> res = mcflt.run() # doctest: +SKIP
>>> mcflt = fsl.MCFLIRT()
>>> mcflt.inputs.in_file = 'functional.nii'
>>> mcflt.inputs.cost = 'mutualinfo'
>>> mcflt.inputs.out_file = 'moco.nii'
>>> mcflt.cmdline # doctest: +ALLOW_UNICODE
'mcflirt -in functional.nii -cost mutualinfo -out moco.nii'
>>> res = mcflt.run() # doctest: +SKIP

"""
_cmd = 'mcflirt'
Expand Down Expand Up @@ -908,6 +913,9 @@ class FNIRTOutputSpec(TraitedSpec):
class FNIRT(FSLCommand):
"""Use FSL FNIRT for non-linear registration.

For complete details, see the `FNIRT Documentation.
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT>`_

Examples
--------
>>> from nipype.interfaces import fsl
Expand Down Expand Up @@ -1208,6 +1216,9 @@ class SUSANOutputSpec(TraitedSpec):
class SUSAN(FSLCommand):
""" use FSL SUSAN to perform smoothing

For complete details, see the `SUSAN Documentation.
<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SUSAN>`_

Examples
--------

Expand Down