Hi everyone,
I have created a DataLad dataset for fMRIPrep data and run fMRIPrep. Now, I wanted to run datalad save to save all the files but I encounter the following problems:
First, apparently DataLad does not manage to save these files: brainmask.mgz and brainmask.auto.mgz. I realize it might be related to this issue that I encountered before for a different dataset and seems to relate to the NFS partition of our HPC. Then again, I am not sure how to tackle this issue? Move the files in a different way and then add to DataLad?
Second, after running datalad save I get a long output of files that looks like this
fmriprep/sub-02/ses-tilt20negative/func/sub-02_ses-tilt20negative_task-planetgems_rec-prenorm_run-03_space-T1w_desc-aseg_dseg.nii.gz
fmriprep/sub-03/ses-tilt20negative/func/sub-03_ses-tilt20negative_task-zootask_rec-prenorm_run-02_space-fsaverage_hemi-L.func.gii
freesurfer/sub-02/touch/rh.jacobian_white.touch
fmriprep/sub-02/ses-tilt20positive/func/sub-02_ses-tilt20positive_task-planetgems_rec-prenorm_run-03_space-MNI152NLin2009cAsym_boldref.nii.gz
fmriprep/sub-03/anat/sub-03_hemi-L_smoothwm.surf.gii
fmriprep/sub-05/ses-tilt20positive/func/sub-05_ses-tilt20positive_task-zootask_rec-prenorm_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
fmriprep/sub-02/ses-tilt20negative/func/sub-02_ses-tilt20negative_task-zootask_rec-prenorm_run-03_space-T1w_desc-aseg_dseg.nii.gz
freesurfer/sub-05/touch/rh.tessellate.touch
freesurfer/sub-05/label/lh.BA4a_exvivo.thresh.label freesurfer/sub-02/scripts/recon-all-rh.cmd freesurfer/sub-05/label/lh.V1_exvivo.thresh.label'
failed with exitcode 1 [File(s) unknown to git]
and (to highlight) ends with failed with exitcode 1 [File(s) unknown to git]. Does this tell me that git does not know how to handle these files? Is this related to the dataset configuration? I think I have initalized with -c text2git but then switched to cfg_bids using datalad run-procedure cfg_bids.
If I run datalad status I get a long output, that seems to tell me that a lot of files are added (but not committed?), see here (truncated and slightly modified):
added: /path/to/project/freesurfer/sub-05/touch/segstats.touch (file)
added: /path/to/project/freesurfer/sub-05/touch/talairach.touch (file)
added: /path/to/project/freesurfer/sub-05/touch/wmaparc.stats.touch (file)
added: /path/to/project/freesurfer/sub-05/touch/wmaparc.touch (file)
added: /path/to/project/freesurfer/sub-05/touch/wmsegment.touch (file)
Any help would be very appreciated. Thanks in advance!