micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
When running micapipe v. 0.2.3 and using pre-run fast or freesurfer and then running -proc_surf, I get the following error:
[ INFO ]..... Creating proc_surf json file
Image Exception : #63 :: No image files match: /xdisk/adamraikes/bids/derivatives/micapipe_0.2.3/fastsurfer/sub-xxx_ses-yy/mri/orig.mgz
No image files match: /xdisk/adamraikes/bids/derivatives/micapipe_0.2.3/fastsurfer/sub-xxx_ses-yy/mri/orig.mgz
Image Exception : #63 :: No image files match: /xdisk/adamraikes/bids/derivatives/micapipe_0.2.3/fastsurfer/sub-xxx_ses-yy/mri/orig.mgz
No image files match: /xdisk/adamraikes/bids/derivatives/micapipe_0.2.3/fastsurfer/sub-xxx_ses-yy/mri/orig.mgz
It's due to the following line where you are overwriting t1_2proc with the orig.mgz file and then attempting to run fslhd and mrinfo on that file instead of a NIFTI. This is different from the behavior when running fast or freesurfer within the container.
Recommend clarifying that when using preprocessed outputs, users must specify the T1w file that was used and then removing this line.
For clarity, I ran fastsurfer externally using the T1nativepro file but fastsurfer v. 2.2.0 with the output directory as ${out}/fastsurfer, so all of the outputs are there and where they are expected to be.
Hello,
When running micapipe v. 0.2.3 and using pre-run fast or freesurfer and then running -proc_surf, I get the following error:
It's due to the following line where you are overwriting t1_2proc with the orig.mgz file and then attempting to run
fslhdandmrinfoon that file instead of a NIFTI. This is different from the behavior when running fast or freesurfer within the container.https://github.com/MICA-MNI/micapipe/blob/0a4315012128aafbe3dfeeeff969bd9b0f4abd15/functions/01_proc-surf.sh#L117
Recommend clarifying that when using preprocessed outputs, users must specify the T1w file that was used and then removing this line.
For clarity, I ran fastsurfer externally using the T1nativepro file but fastsurfer v. 2.2.0 with the output directory as ${out}/fastsurfer, so all of the outputs are there and where they are expected to be.