mapnode trouble

[binarybottle]

pipeline.py lines 189-190:

flo1.connect([(atlas_reg, majority_vote,
[('output_file', 'annot_files')])])

atlas_reg's register_atlas() function and majority_vote's multilabel() function aren't connecting properly here. multilabel() is printing the annot_files list as ['U','U'] instead of the annot file names.

(commit 4fbef6e)

[satra]

can you paste the output of report.rst from the 'Register_atlases' node? specifically the inputs and outputs sections.

[binarybottle]

Node: Atlas_workflow (Register_atlases (utility)

Hierarchy : Mindboggle_workflow.Atlas_workflow.Register_atlases
Exec ID : Register_atlases.a0

Original Inputs

• atlas_annot_name : aparcNMMjt.annot
• atlas_name : ['KKI2009-14', 'KKI2009-15']
• atlases_path : /Applications/freesurfer/subjects
• function_str : S'def register_atlas(hemi, subject_id,
  template_reg_name,\n atlas_name, atlases_path,
  atlas_annot_name):\n """\n Transform the labels from multiple atlases
  via a template\n using FreeSurfer's mri_surf2surf (wrapped in
  NiPype)\n\n nipype.workflows.smri.freesurfer.utils.fs.SurfaceTransform\n
  wraps command mri_surf2surf:\n "Transform a surface file from one
  subject to another via a spherical registration.\n Both the source and
  target subject must reside in your Subjects Directory,\n and they must
  have been processed with recon-all, unless you are transforming\n to one
  of the icosahedron meshes."\n """\n from os import path, getcwd\n
  from nipype.interfaces.freesurfer import SurfaceTransform\n\n sxfm =
  SurfaceTransform()\n sxfm.inputs.hemi = hemi\n
  sxfm.inputs.target_subject = subject_id\n sxfm.inputs.source_subject =
  atlas_name\n\n # Source file\n sxfm.inputs.source_annot_file =
  path.join(atlases_path, \n atlas_name,
  'label',\n hemi + '.' +
  atlas_annot_name) \n # Output annotation file\n output_file =
  path.join(getcwd(), hemi + '.' + atlas_name + 'to' + \n
  subject_id + '_' + atlas_annot_name)\n
  sxfm.inputs.out_file = output_file\n\n # Arguments: strings within
  registered files\n args = ['--srcsurfreg', template_reg_name,\n
  '--trgsurfreg', template_reg_name]\n sxfm.inputs.args = '
  '.join(args)\n\n sxfm.run()\n\n return output_file\n'
  .
• hemi :
• ignore_exception : False
• subject_id :
• template_reg_name :

Execution Inputs

• atlas_annot_name : aparcNMMjt.annot
• atlas_name : ['KKI2009-14', 'KKI2009-15']
• atlases_path : /Applications/freesurfer/subjects
• function_str : S'def register_atlas(hemi, subject_id,
  template_reg_name,\n atlas_name, atlases_path,
  atlas_annot_name):\n """\n Transform the labels from multiple atlases
  via a template\n using FreeSurfer's mri_surf2surf (wrapped in
  NiPype)\n\n nipype.workflows.smri.freesurfer.utils.fs.SurfaceTransform\n
  wraps command mri_surf2surf:\n "Transform a surface file from one
  subject to another via a spherical registration.\n Both the source and
  target subject must reside in your Subjects Directory,\n and they must
  have been processed with recon-all, unless you are transforming\n to one
  of the icosahedron meshes."\n """\n from os import path, getcwd\n
  from nipype.interfaces.freesurfer import SurfaceTransform\n\n sxfm =
  SurfaceTransform()\n sxfm.inputs.hemi = hemi\n
  sxfm.inputs.target_subject = subject_id\n sxfm.inputs.source_subject =
  atlas_name\n\n # Source file\n sxfm.inputs.source_annot_file =
  path.join(atlases_path, \n atlas_name,
  'label',\n hemi + '.' +
  atlas_annot_name) \n # Output annotation file\n output_file =
  path.join(getcwd(), hemi + '.' + atlas_name + 'to' + \n
  subject_id + '_' + atlas_annot_name)\n
  sxfm.inputs.out_file = output_file\n\n # Arguments: strings within
  registered files\n args = ['--srcsurfreg', template_reg_name,\n
  '--trgsurfreg', template_reg_name]\n sxfm.inputs.args = '
  '.join(args)\n\n sxfm.run()\n\n return output_file\n'
  .
• hemi :
• ignore_exception : False
• subject_id :
• template_reg_name :

Execution Outputs

• output_file : ['U', 'U']

[satra]

seems to me that you have a lot of inputs that are not defined.

[binarybottle]

how odd -- i ran the same code on my linux machine and it worked!

[satra]

i think you have some strange python setup going on. you should have a clean install of things. if you don't resolve those issues debugging might become more painful.

[binarybottle]

i removed all old versions of nipype and nibabel and now have everything working on linux and osx.