Mindboggle error during explode_scalars

[araikes]

Hi, I am running Mindboggle on some data that I have already processed through Freesurfer and ANTs. I'm running Mindboggle from within the Docker container. I've also set up a script file to loop through all of my participants.

I'm running the mindboggle command as follows (No moments or spectra for speed purposes): mindboggle $FS/${subj} --ants $ANTS_DIR/${subj}/Segmentation/BrainSegmentation.nii.gz --out $MB_DIR --roygbiv --no_moments --no_spectra

I get an error when exploding the labels for roygbiv. I'm attaching one of the crash files.

I was also getting the affine dimension error, so I have already updated configparser and nipype.

Any help you can be would be great. crash-20171004-170135-jovyan-Explode_Labels.a1-caf36b95-c72a-4412-91c4-eb0b3311db12.zip

[binarybottle]

For clarity, here is the error I received while looking at your crash file:

jovyan@74d48dabb7aa:~/work/Desktop$ nipypecli crash crash-20171004-170135-jovyan-Explode_Labels.a1-caf36b95-c72a-4412-91c4-eb0b3311db12.pklz

File: /home/jovyan/work/Desktop/crash-20171004-170135-jovyan-Explode_Labels.a1-caf36b95-c72a-4412-91c4-eb0b3311db12.pklz Node: Mindboggle.Explode_Labels.a1 Working directory: /home/jovyan/work/BIDS/Chronic_mTBI/MindBoggled/working/sub-mTBI113/Mindboggle/_hemi_rh/Explode_Labels

Node inputs: ...

ignore_exception = False input_indices_vtk = /data/TBIMODEL/group_analysis/Adam/BIDS/Chronic_mTBI/MindBoggled/working/sub-mTBI113/Mindboggle/Surface_labels/_hemi_rh/Reindex_labels/relabeled_rh.aparc.vtk input_values_vtk = output_scalar_name = scalars output_stem = label reindex = True remove_background_faces = True verbose = True

Traceback: Traceback (most recent call last): File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/plugins/linear.py", line 43, in run node.run(updatehash=updatehash) File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py", line 372, in run self._run_interface() File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py", line 482, in _run_interface self._result = self._run_command(execute) File "/opt/conda/lib/python3.5/site-packages/nipype/pipeline/engine/nodes.py", line 613, in _run_command result = self._interface.run() File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py", line 1081, in run runtime = self._run_wrapper(runtime) File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py", line 1029, in _run_wrapper runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/utility/wrappers.py", line 194, in _run_interface out = function_handle(**args) File "", line 92, in explode_scalars File "/opt/conda/lib/python3.5/site-packages/mindboggle/mio/vtks.py", line 384, in read_vtk PointData = Data.GetPointData() AttributeError: 'NoneType' object has no attribute 'GetPointData' Interface Function failed to run.

[binarybottle]

The following error suggests that the your relabeled right hemisphere surface file is not correct:

AttributeError: 'NoneType' object has no attribute 'GetPointData'

Would you please share the file?:

input_indices_vtk = /data/TBIMODEL/group_analysis/Adam/BIDS/Chronic_mTBI/MindBoggled/working/sub-mTBI113/Mindboggle/Surface_labels/_hemi_rh/Reindex_labels/relabeled_rh.aparc.vtk

[binarybottle]

@araikes -- Were you able to figure out why your FreeSurfer inputs were not working? If not, I am happy to look at the file that was causing the problem.

[binarybottle]

@araikes -- Just touching base about this issue. Were you able to resolve it, and if not, could you please share the relabeled_rh.aparc.vtk file? If I don't hear back, I'll assume that this issue has been resolved or was a problem related to the FreeSurfer run, given that read_vtk() couldn't find any points in the right surface mesh...