Are you there, God? It’s me, Ivan.
I have been encountering issues during preprocessing in the following nodes:
I originally ran this on version 21.0.2 and 21.0.1. No dice. I have attached the full crash reports here.
One possible culprit is not including some path after the -B flag in singularity, but I’m a little clueless. Here is the singularity call:
singularity run --cleanenv -B /tmp,/data/p_SoftwareServiceLinux_sc/fmriprep/21.0.2/1,/data/pt_02577/fmriprep_work/,/data/pt_02577/BIDS_dataset/inputs/,/data/pt_02577/BIDS_dataset/derivatives/,/afs/cbs/software/freesurfer/:/afs/cbs/software/freesurfer/licensekeys /data/p_SoftwareServiceLinux_sc/fmriprep/21.0.2/1 /data/pt_02577/BIDS_dataset/inputs/ /data/pt_02577/BIDS_dataset/derivatives/ --n_cpus 2 participant --participant-label 201 --work-dir /data/pt_02577/fmriprep_work/ --fs-license-file /afs/cbs.mpg.de/software/freesurfer/licensekeys --verbose --output-layout legacy --resource-monitor --fs-no-reconall --skip_bids_validation
crash-20220623-093928-krasovec-norm-62aa8e50-14bf-40d8-9597-4977d85f66b8.txt (3.9 KB)
crash-20220623-085257-krasovec-unifize-009f794a-26df-418e-8838-8d64c54cf61a.txt (2.3 KB)
A few suggestions:
- It is not clear why there are so many things being bound to the container. It seems like you could get away just binding
- You have an argument
--fs-license-file /afs/cbs.mpg.de/software/freesurfer/licensekeys. That sounds like the name of a directory, and not a FS lincense txt file. Make sure that whatever goes there points to a valid FS license.
--fs-no-reconall is discouraged. See here.
- Can you confirm that the container was built properly?
So, try something like this:
singularity run --cleanenv -B /data,/afs /data/p_SoftwareServiceLinux_sc/fmriprep/21.0.2/1 \
/data/pt_02577/BIDS_dataset/inputs/ /data/pt_02577/BIDS_dataset/derivatives/ \
--n_cpus 2 participant --participant-label 201 --work-dir /data/pt_02577/fmriprep_work/ \
--fs-license-file /afs/cbs.mpg.de/software/freesurfer/licensekeys \
--verbose --output-layout legacy --resource-monitor --skip_bids_validation
Thank you for your response!
- I agree with the minimal approach. Singularity and fmriprep were happy to eat the simplified command, and the complaint regarding the python path was resolved.
- The –fs-license-file path points to the license file for our institution. It otherwise works and I do not get a license error.
- I incurred Talairach errors in the past and, until I manually correct those, I am working on getting the code running without reconall more as a proof of concept and to debug any other errors that pop up (and good heavens, there are many). Overall though, I do agree with keeping reconall.
- Since correcting the command, I’ll leave the container alone for now.
Thank you again for your input. I also wanted to mention that I see that there is a lot of activity and discussions on Neurostars and GitHub and you all are really wonderful about giving in-depth and informative answers. You guys do good work!