@@ -118,15 +118,17 @@ class BET(FSLCommand):
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"""Use FSL BET command for skull stripping.
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For complete details, see the `BET Documentation.
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- <http ://www .fmrib.ox.ac.uk/fsl/bet2/index.html >`_
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+ <https ://fsl .fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide >`_
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Examples
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--------
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>>> from nipype.interfaces import fsl
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- >>> from nipype.testing import example_data
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>>> btr = fsl.BET()
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- >>> btr.inputs.in_file = example_data( 'structural.nii')
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+ >>> btr.inputs.in_file = 'structural.nii'
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>>> btr.inputs.frac = 0.7
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+ >>> btr.inputs.out_file = 'brain_anat.nii'
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+ >>> btr.cmdline # doctest: +ALLOW_UNICODE
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+ 'bet structural.nii brain_anat.nii -f 0.70'
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>>> res = btr.run() # doctest: +SKIP
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"""
@@ -275,7 +277,7 @@ class FASTOutputSpec(TraitedSpec):
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mixeltype = File (desc = "path/name of mixeltype volume file _mixeltype" )
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- partial_volume_map = File (desc = " path/name of partial volume file _pveseg" )
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+ partial_volume_map = File (desc = ' path/name of partial volume file _pveseg' )
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partial_volume_files = OutputMultiPath (File (
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desc = 'path/name of partial volumes files one for each class, _pve_x' ))
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@@ -288,18 +290,17 @@ class FAST(FSLCommand):
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""" Use FSL FAST for segmenting and bias correction.
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For complete details, see the `FAST Documentation.
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- <http ://www .fmrib.ox.ac.uk/fsl/fast4/index.html >`_
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+ <https ://fsl .fmrib.ox.ac.uk/fsl/fslwiki/FAST >`_
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Examples
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--------
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>>> from nipype.interfaces import fsl
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- >>> from nipype.testing import example_data
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-
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- Assign options through the ``inputs`` attribute:
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-
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>>> fastr = fsl.FAST()
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- >>> fastr.inputs.in_files = example_data('structural.nii')
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- >>> out = fastr.run() #doctest: +SKIP
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+ >>> fastr.inputs.in_files = 'structural.nii'
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+ >>> fastr.inputs.out_basename = 'fast_'
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+ >>> fastr.cmdline # doctest: +ALLOW_UNICODE
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+ 'fast -o fast_ -S 1 structural.nii'
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+ >>> out = fastr.run() # doctest: +SKIP
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"""
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_cmd = 'fast'
@@ -308,12 +309,12 @@ class FAST(FSLCommand):
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def _format_arg (self , name , spec , value ):
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# first do what should be done in general
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- formated = super (FAST , self )._format_arg (name , spec , value )
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+ formatted = super (FAST , self )._format_arg (name , spec , value )
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if name == 'in_files' :
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# FAST needs the -S parameter value to correspond to the number
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# of input images, otherwise it will ignore all but the first
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- formated = "-S %d %s" % (len (value ), formated )
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- return formated
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+ formatted = "-S %d %s" % (len (value ), formatted )
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+ return formatted
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def _list_outputs (self ):
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outputs = self .output_spec ().get ()
@@ -526,7 +527,7 @@ class FLIRT(FSLCommand):
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"""Use FSL FLIRT for coregistration.
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For complete details, see the `FLIRT Documentation.
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- <http ://www .fmrib.ox.ac.uk/fsl/flirt/index.html >`_
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+ <https ://fsl .fmrib.ox.ac.uk/fsl/fslwiki/FLIRT >`_
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To print out the command line help, use:
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fsl.FLIRT().inputs_help()
@@ -655,14 +656,18 @@ class MCFLIRT(FSLCommand):
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"""Use FSL MCFLIRT to do within-modality motion correction.
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For complete details, see the `MCFLIRT Documentation.
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- <http ://www .fmrib.ox.ac.uk/fsl/mcflirt/index.html >`_
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+ <https ://fsl .fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT >`_
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Examples
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--------
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>>> from nipype.interfaces import fsl
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- >>> from nipype.testing import example_data
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- >>> mcflt = fsl.MCFLIRT(in_file=example_data('functional.nii'), cost='mutualinfo')
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- >>> res = mcflt.run() # doctest: +SKIP
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+ >>> mcflt = fsl.MCFLIRT()
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+ >>> mcflt.inputs.in_file = 'functional.nii'
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+ >>> mcflt.inputs.cost = 'mutualinfo'
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+ >>> mcflt.inputs.out_file = 'moco.nii'
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+ >>> mcflt.cmdline # doctest: +ALLOW_UNICODE
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+ 'mcflirt -in functional.nii -cost mutualinfo -out moco.nii'
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+ >>> res = mcflt.run() # doctest: +SKIP
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"""
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_cmd = 'mcflirt'
@@ -908,6 +913,9 @@ class FNIRTOutputSpec(TraitedSpec):
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class FNIRT (FSLCommand ):
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"""Use FSL FNIRT for non-linear registration.
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+ For complete details, see the `FNIRT Documentation.
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+ <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT>`_
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+
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Examples
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--------
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>>> from nipype.interfaces import fsl
@@ -1208,6 +1216,9 @@ class SUSANOutputSpec(TraitedSpec):
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class SUSAN (FSLCommand ):
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""" use FSL SUSAN to perform smoothing
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+ For complete details, see the `SUSAN Documentation.
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+ <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SUSAN>`_
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+
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Examples
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--------
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