Can not specify own_atlas in CAT12Segment #3562
Description
Summary
I'm trying to use aal3.nii as own atlas in CAT12Segment:
seg.inputs.own_atlas = [os.path.abspath(os.path.join('data', 'bin', 'aal3.nii'))]But after adding this line, an error occurred when running the matlab script:
Unable to perform assignment because the left and right sides have a different number of elements The generated code is:
jobs{1}.spm.tools.cat.estwrite.output.ROImenu.atlases.ownatlas(1) = '/abs/path/to/workflow/cat12segment/subj_id/seg/aal3.nii';Actual behavior
CAT12Segment can not proceed.
Expected behavior
Segmentation with aal labels
How to replicate the behavior
Specify the value of own_atlas
Script/Workflow details
data = getPandas('pat_data').iloc[:1] key_list = data['KEY'].tolist() wf = Workflow(name='cat12segment', base_dir=os.path.abspath('tmp')) info_src = Node(util.IdentityInterface(fields=['key']), name='info_src') info_src.iterables = ('key', key_list) raw_src = Node(nio.DataGrabber(infields=['key'], outfields=['raw']), name='raw_src') raw_src.inputs.base_directory = os.path.abspath(os.path.join('data', 'subj')) raw_src.inputs.sort_filelist = False raw_src.inputs.template = '*' raw_src.inputs.template_args = { 'raw': [['key']] } raw_src.inputs.field_template = { 'raw': os.path.join('%s', 'raw', 'raw.nii') } seg = Node(CAT12Segment(), name='seg') seg.inputs.own_atlas = [os.path.abspath(os.path.join('data', 'bin', 'aal3.nii'))] sink = Node(nio.DataSink(), name='sink') sink.inputs.base_directory = os.path.abspath(os.path.join('data', 'subj')) sink.inputs.parameterization = False wf.connect([ (info_src, raw_src, [('key', 'key')]), (raw_src, seg, [('raw', 'in_files')]), (info_src, sink, [('key', 'container')]), (seg, sink, [ ('gm_modulated_image', 'cat12.mri.@gm'), ('wm_modulated_image', 'cat12.mri.@wm'), ('csf_modulated_image', 'cat12.mri.@csf'), ('mri_images', 'cat12.mri.@mri_images'), ('label_files', 'cat12.label.@label_files'), ('label_roi', 'cat12.label.@label_roi'), ('label_rois', 'cat12.label.@label_rois'), ('lh_central_surface', 'cat12.surf.@lh_central_surface'), ('lh_sphere_surface', 'cat12.surf.@lh_sphere_surface'), ('rh_central_surface', 'cat12.surf.@rh_central_surface'), ('rh_sphere_surface', 'cat12.surf.@rh_sphere_surface'), ('report_files', 'cat12.report.@report_files'), ('report', 'cat12.report.@report'), ('surface_files', 'cat12.surf.@surface_files'), ]), ]) wf.run()Platform details:
{'commit_hash': 'dd60d5f', 'commit_source': 'repository', 'networkx_version': '2.5', 'nibabel_version': '5.0.0', 'nipype_version': '1.8.5', 'numpy_version': '1.24.1', 'pkg_path': '/home/biobot/.pyenv/versions/3.10.9/lib/python3.10/site-packages/nipype', 'scipy_version': '1.10.0', 'sys_executable': '/home/biobot/.pyenv/versions/3.10.9/bin/python', 'sys_platform': 'linux', 'sys_version': '3.10.9 (main, Jan 29 2023, 21:28:03) [GCC 11.3.0]', 'traits_version': '6.3.2'} Execution environment
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