Only getting anat output for fmriprep

1

Hi, I am only receiving anatomical derivatives as output for fmriprep, how can i get functional derivatives also? Using this dataset.

i am running command

singularity exec fmriprep-1.1.4.simg fmriprep /fastdata/aca16mha/raiders /data/aca16mha/results participant --participant-label rid000005

2

Can you show a tree of your outputs? What is the output of fmriprep, can you attach the full log?

It seems that the processing may still be going on, or maybe it crashed with error.

3

I think it may have crashed as it says on log preprocessing was undertaken for the 8 BOLD runs, I will do a fresh run to check. Is it possible to resume fmriprep if it crashes?

CITATION.txt (13.4 KB)

4

Yes, please make sure of capturing the output log (maybe you can redirect the output to a file?)

singularity run fmriprep-1.1.4.simg \
    /fastdata/aca16mha/raiders \
    /data/aca16mha/results \
    participant --participant-label rid000005 &> log.txt

I say this because the file you posted above is just the text of the citation boilerplate, not the output log (although it is found in a folder called log/, which can be confusing).

If you reuse your work directory, yes. The previous run should’ve created a work/ directory under the directory where you invoked singularity exec. If you re-run again from that folder, it should pick it up.