I’m running fmriprep for the first time and haven’t managed to get a full output yet - I would really appreciate any thoughts on these issues. I may have fundamentally misunderstood some things!
Here are the two commands I have tried, the latter since finding a possible solution for the amd64 problem on the M1 mac:
fmriprep-docker /Users/z/…/T2/ABM_test /Users/z/…/T2/testprep --fs-license-file $HOME/license.txt
docker run --platform linux/amd64 --rm -e DOCKER_VERSION_8395080871=20.10.17 -it -v /Users/z/license.txt:/opt/freesurfer/license.txt:ro -v /Users/z/…/T2/ABM_test:/data:ro -v /Users/z/…/T2/testprep:/out nipreps/fmriprep:22.0.2 /data /out participant
Here is the folder structure, which passes a BIDS validation and is intentionally minimal with one run of one task (although it may be less than the minimum files needed for fMRIPrep to run):
│ ├── sub-01_T1w.json
│ └── sub-01_T1w.nii.gz
The final message I get before it hangs indefinitely (<24hrs before I end it):
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 1.99/6.99, Free processors: 1/6.
Is it possible that the machine I’m using is just not powerful enough? I get a warning saying “Some nodes exceed the total amount of memory available (8.75GB).”, which I took to mean it would take longer than usual, but perhaps it means it’s simply not possible. I have 16GB RAM and the full folder structure is 2.17GB. I may also have neglected to include some necessary things in the dataset, which is leading it to halt as the expected files aren’t there.
Very new to this so hopefully I have included the necessary things in this post, but please do let me know if not. Thanks in advance!