nipy/nipype — pull request #738 by swederik (2013-12-02 12:18:16+00:00)
Title: BF: Fixing path issues for CMTK Parcellate dilated ROI files

Some cleanup of the CMTK Parcellate interface to fix

Seems that the

op.join(op.curdir, "blah"...

wasn't working properly. Just replaced it with:

op.abspath("blah")

and removed some unused variables.

Tested with:

import nipype.interfaces.cmtk as cmtk
import os
import nipype.pipeline.engine as pe # pypeline engine
a = pe.Node(interface=cmtk.Parcellate(), name="testparc")
a.base_dir = "testparcnode"
a.inputs.subject_id = "bert"
a.inputs.subjects_dir = os.environ["SUBJECTS_DIR"]
a.inputs.dilation = False
a.inputs.parcellation_name = "scale33"
a.run()

There shouldn't be any differences in outputs for the other parcellation scales.

Should give a report.rest with inputs/outputs like this (github markdown seems to hide < undefined >):

Original Inputs
---------------

* dilation : True
* freesurfer_dir :
* ignore_exception : False
* out_roi_file :
* parcellation_name : scale33
* subject_id : bert
* subjects_dir : /Applications/freesurfer/subjects

Execution Inputs
----------------

* dilation : True
* freesurfer_dir :
* ignore_exception : False
* out_roi_file :
* parcellation_name : scale33
* subject_id : bert
* subjects_dir : /Applications/freesurfer/subjects

Execution Outputs
-----------------

* aseg_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc/aseg.nii.gz
* cc_unknown_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc/cc_unknown.nii.gz
* dilated_roi_file_in_structural_space : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc/ROIv_HR_th.nii.gz
* ribbon_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc/ribbon.nii.gz
* roi_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc/ROI_scale33.nii.gz
* roi_file_in_structural_space : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc/ROI_HR_th.nii.gz
* roiv_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc/ROIv_scale33.nii.gz
* white_matter_mask_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc/fsmask_1mm.nii.gz

# For no Dilation:

Original Inputs
---------------

* dilation : False
* freesurfer_dir :
* ignore_exception : False
* out_roi_file :
* parcellation_name : scale33
* subject_id : bert
* subjects_dir : /Applications/freesurfer/subjects

Execution Inputs
----------------

* dilation : False
* freesurfer_dir :
* ignore_exception : False
* out_roi_file :
* parcellation_name : scale33
* subject_id : bert
* subjects_dir : /Applications/freesurfer/subjects

Execution Outputs
-----------------

* aseg_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc_nodil/aseg.nii.gz
* cc_unknown_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc_nodil/cc_unknown.nii.gz
* dilated_roi_file_in_structural_space :
* ribbon_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc_nodil/ribbon.nii.gz
* roi_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc_nodil/ROI_scale33.nii.gz
* roi_file_in_structural_space : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc_nodil/ROI_HR_th.nii.gz
* roiv_file :
* white_matter_mask_file : /Users/erik/Dropbox/Testing/testparc/testparcnode/testparc_nodil/fsmask_1mm.nii.gz