Multi-Scale Brain Parcellator, part of the Connectome Mapping Toolkit (CMTK), is a BIDS App that implements a full anatomical MRI processing pipeline, from raw T1w data to structural brain parcellation at five different scales.
I'm running the MSBP pipeline on apptainer using the following command, 'multiscalebrainparcellator_bidsapp_entrypointscript /path2bids_dir /path2_output_dir/ participant --participant_label C099 --isotropic_resolution 0.6 --thalamic_nuclei --hippocampal_subfields --brainstem_structures --skip_bids_validator and I get the following error,
'File "/opt/conda/lib/python2.7/site-packages/cmtklib/parcellation.py", line 2704, in crop_and_move_datasets
raise Exception('File %s does not exist.' % d[0])
Exception: File /home/naxos2-raid14/jayashre/bids_ctrl_data/Nifti/derivatives/freesurfer/sub-C099_ses-7T/mri/ROIv_scale4.nii.gz does not exist.'
I'm not sure how to go about resolving this (log attached). Please let me know if you need more info. Appreciate your help!
pypeline.log
jayashree15
commented
1 year ago
Hello,
I'm running the MSBP pipeline on apptainer using the following command, 'multiscalebrainparcellator_bidsapp_entrypointscript /path2bids_dir /path2_output_dir/ participant --participant_label C099 --isotropic_resolution 0.6 --thalamic_nuclei --hippocampal_subfields --brainstem_structures --skip_bids_validator and I get the following error,
'File "/opt/conda/lib/python2.7/site-packages/cmtklib/parcellation.py", line 2704, in crop_and_move_datasets raise Exception('File %s does not exist.' % d[0]) Exception: File /home/naxos2-raid14/jayashre/bids_ctrl_data/Nifti/derivatives/freesurfer/sub-C099_ses-7T/mri/ROIv_scale4.nii.gz does not exist.'
I'm not sure how to go about resolving this (log attached). Please let me know if you need more info. Appreciate your help! pypeline.log
Jayashree