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David Ellis
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FIX: Removes unused functions and imports.
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-174
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4 files changed

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‎nipype/workflows/smri/freesurfer/autorecon1.py‎

Lines changed: 1 addition & 4 deletions
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@@ -1,10 +1,7 @@
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import sys
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import os
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import nipype
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from nipype.interfaces.utility import Function,IdentityInterface
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import nipype.pipeline.engine as pe # pypeline engine
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from nipype.interfaces.freesurfer import *
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from .utils import copy_file, copy_files
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from .utils import copy_file
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def checkT1s(T1_files, cw256=False):

‎nipype/workflows/smri/freesurfer/autorecon2.py‎

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@@ -1,5 +1,3 @@
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import os
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import nipype
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from nipype.interfaces.utility import Function, IdentityInterface, Merge
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import nipype.pipeline.engine as pe # pypeline engine
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from nipype.interfaces.freesurfer import *

‎nipype/workflows/smri/freesurfer/autorecon3.py‎

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,7 @@
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import os
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import nipype
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from nipype.interfaces.utility import Function, IdentityInterface, Merge
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from nipype.interfaces.utility import IdentityInterface, Merge
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import nipype.pipeline.engine as pe # pypeline engine
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from nipype.interfaces.freesurfer import *
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from .ba_maps import create_ba_maps_wf
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from .utils import createsrcsubj
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from nipype.interfaces.io import DataGrabber
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def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,

‎nipype/workflows/smri/freesurfer/utils.py‎

Lines changed: 0 additions & 164 deletions
Original file line numberDiff line numberDiff line change
@@ -492,167 +492,3 @@ def checkenv(exitonfail=False):
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sys.exit(2)
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else:
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print("Warning: " + msg)
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def create_recoding_wf(in_file, out_file=None):
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wf = nipype.Workflow(name="RecodeLabels")
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inputspec = nipype.pipeline.Node(nipype.IdentityInterface(['labelmap',
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'recode_file']),
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name="inputspec")
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inputspec.inputs.recode_file = in_file
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convert_labelmap = nipype.pipeline.Node(fs.MRIConvert(), name="ConvertLabelMap")
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convert_labelmap.inputs.in_type = 'mgz'
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convert_labelmap.inputs.out_type = 'nii'
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convert_labelmap.inputs.out_orientation = 'RAS'
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convert_labelmap.inputs.out_file = 'labelmap.nii'
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wf.connect([(inputspec, convert_labelmap, [('labelmap', 'in_file')])])
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recode = nipype.Node(nipype.Function(['in_file',
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'out_file',
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'recode_file'],
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['out_file'],
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recodeLabelMap),
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name = "RecodeLabelMap")
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if out_file == None:
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recode.inputs.out_file = 'recodedlabelmap.nii'
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else:
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recode.inputs.out_file = out_file
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wf.connect([(convert_labelmap, recode, [('out_file', 'in_file')]),
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(inputspec, recode, [('recode_file', 'recode_file')])])
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center_labelmap = nipype.Node(nipype.Function(['in_file'], ['out_file'],
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center_volume),
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name="CenterLabelMap")
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wf.connect([(recode, center_labelmap, [('out_file', 'in_file')])])
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outputspec = nipype.Node(nipype.IdentityInterface(['recodedlabelmap']), name="outputspec")
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wf.connect([(center_labelmap, outputspec, [('out_file', 'recodedlabelmap')])])
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return wf
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def createsrcsubj(source_directory):
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"""
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Returns a node that acts as the datasource for a source subject such as
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'fsaverage'
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"""
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outfields = ['lh_BA1_exvivo',
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'lh_BA2_exvivo',
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'lh_BA3a_exvivo',
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'lh_BA3b_exvivo',
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'lh_BA4a_exvivo',
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'lh_BA4p_exvivo',
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'lh_BA6_exvivo',
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'lh_BA44_exvivo',
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'lh_BA45_exvivo',
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'lh_V1_exvivo',
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'lh_V2_exvivo',
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'lh_MT_exvivo',
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'lh_entorhinal_exvivo',
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'lh_perirhinal_exvivo',
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'lh_BA1_exvivo_thresh',
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'lh_BA2_exvivo_thresh',
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'lh_BA3a_exvivo_thresh',
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'lh_BA3b_exvivo_thresh',
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'lh_BA4a_exvivo_thresh',
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'lh_BA4p_exvivo_thresh',
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'lh_BA6_exvivo_thresh',
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'lh_BA44_exvivo_thresh',
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'lh_BA45_exvivo_thresh',
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'lh_V1_exvivo_thresh',
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'lh_V2_exvivo_thresh',
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'lh_MT_exvivo_thresh',
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'lh_entorhinal_exvivo_thresh',
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'lh_perirhinal_exvivo_thresh',
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'rh_BA1_exvivo',
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'rh_BA2_exvivo',
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'rh_BA3a_exvivo',
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'rh_BA3b_exvivo',
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'rh_BA4a_exvivo',
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'rh_BA4p_exvivo',
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'rh_BA6_exvivo',
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'rh_BA44_exvivo',
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'rh_BA45_exvivo',
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'rh_V1_exvivo',
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'rh_V2_exvivo',
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'rh_MT_exvivo',
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'rh_entorhinal_exvivo',
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'rh_perirhinal_exvivo',
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'rh_BA1_exvivo_thresh',
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'rh_BA2_exvivo_thresh',
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'rh_BA3a_exvivo_thresh',
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'rh_BA3b_exvivo_thresh',
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'rh_BA4a_exvivo_thresh',
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'rh_BA4p_exvivo_thresh',
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'rh_BA6_exvivo_thresh',
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'rh_BA44_exvivo_thresh',
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'rh_BA45_exvivo_thresh',
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'rh_V1_exvivo_thresh',
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'rh_V2_exvivo_thresh',
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'rh_MT_exvivo_thresh',
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'rh_entorhinal_exvivo_thresh',
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'rh_perirhinal_exvivo_thresh']
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datasource = pe.Node(nio.nio.DataGrabber(outfields=outfields), name="Source_Subject")
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datasource.inputs.base_directory = source_directory
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datasource.inputs.template = '*'
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datasource.inputs.field_template = dict(
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lh_BA1_exvivo='label/lh.BA1_exvivo.label',
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lh_BA2_exvivo='label/lh.BA2_exvivo.label',
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lh_BA3a_exvivo='label/lh.BA3a_exvivo.label',
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lh_BA3b_exvivo='label/lh.BA3b_exvivo.label',
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lh_BA4a_exvivo='label/lh.BA4a_exvivo.label',
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lh_BA4p_exvivo='label/lh.BA4p_exvivo.label',
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lh_BA6_exvivo='label/lh.BA6_exvivo.label',
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lh_BA44_exvivo='label/lh.BA44_exvivo.label',
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lh_BA45_exvivo='label/lh.BA45_exvivo.label',
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lh_V1_exvivo='label/lh.V1_exvivo.label',
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lh_V2_exvivo='label/lh.V2_exvivo.label',
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lh_MT_exvivo='label/lh.MT_exvivo.label',
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lh_entorhinal_exvivo='label/lh.entorhinal_exvivo.label',
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lh_perirhinal_exvivo='label/lh.perirhinal_exvivo.label',
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lh_BA1_exvivo_thresh='label/lh.BA1_exvivo.thresh.label',
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lh_BA2_exvivo_thresh='label/lh.BA2_exvivo.thresh.label',
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lh_BA3a_exvivo_thresh='label/lh.BA3a_exvivo.thresh.label',
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lh_BA3b_exvivo_thresh='label/lh.BA3b_exvivo.thresh.label',
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lh_BA4a_exvivo_thresh='label/lh.BA4a_exvivo.thresh.label',
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lh_BA4p_exvivo_thresh='label/lh.BA4p_exvivo.thresh.label',
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lh_BA6_exvivo_thresh='label/lh.BA6_exvivo.thresh.label',
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lh_BA44_exvivo_thresh='label/lh.BA44_exvivo.thresh.label',
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lh_BA45_exvivo_thresh='label/lh.BA45_exvivo.thresh.label',
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lh_V1_exvivo_thresh='label/lh.V1_exvivo.thresh.label',
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lh_V2_exvivo_thresh='label/lh.V2_exvivo.thresh.label',
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lh_MT_exvivo_thresh='label/lh.MT_exvivo.thresh.label',
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lh_entorhinal_exvivo_thresh='label/lh.entorhinal_exvivo.thresh.label',
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lh_perirhinal_exvivo_thresh='label/lh.perirhinal_exvivo.thresh.label',
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rh_BA1_exvivo='label/rh.BA1_exvivo.label',
631-
rh_BA2_exvivo='label/rh.BA2_exvivo.label',
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rh_BA3a_exvivo='label/rh.BA3a_exvivo.label',
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rh_BA3b_exvivo='label/rh.BA3b_exvivo.label',
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rh_BA4a_exvivo='label/rh.BA4a_exvivo.label',
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rh_BA4p_exvivo='label/rh.BA4p_exvivo.label',
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rh_BA6_exvivo='label/rh.BA6_exvivo.label',
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rh_BA44_exvivo='label/rh.BA44_exvivo.label',
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rh_BA45_exvivo='label/rh.BA45_exvivo.label',
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rh_V1_exvivo='label/rh.V1_exvivo.label',
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rh_V2_exvivo='label/rh.V2_exvivo.label',
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rh_MT_exvivo='label/rh.MT_exvivo.label',
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rh_entorhinal_exvivo='label/rh.entorhinal_exvivo.label',
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rh_perirhinal_exvivo='label/rh.perirhinal_exvivo.label',
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rh_BA1_exvivo_thresh='label/rh.BA1_exvivo.thresh.label',
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rh_BA2_exvivo_thresh='label/rh.BA2_exvivo.thresh.label',
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rh_BA3a_exvivo_thresh='label/rh.BA3a_exvivo.thresh.label',
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rh_BA3b_exvivo_thresh='label/rh.BA3b_exvivo.thresh.label',
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rh_BA4a_exvivo_thresh='label/rh.BA4a_exvivo.thresh.label',
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rh_BA4p_exvivo_thresh='label/rh.BA4p_exvivo.thresh.label',
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rh_BA6_exvivo_thresh='label/rh.BA6_exvivo.thresh.label',
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rh_BA44_exvivo_thresh='label/rh.BA44_exvivo.thresh.label',
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rh_BA45_exvivo_thresh='label/rh.BA45_exvivo.thresh.label',
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rh_V1_exvivo_thresh='label/rh.V1_exvivo.thresh.label',
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rh_V2_exvivo_thresh='label/rh.V2_exvivo.thresh.label',
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rh_MT_exvivo_thresh='label/rh.MT_exvivo.thresh.label',
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rh_entorhinal_exvivo_thresh='label/rh.entorhinal_exvivo.thresh.label',
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rh_perirhinal_exvivo_thresh='label/rh.perirhinal_exvivo.thresh.label')
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return datasource, outfields

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