Hi all,
For some reason, my fmriprep html output does not include the summary, anatomical, and functional sections, although the figures for these sections are created in separate files and there are no errors to report.
I am very new to fmriprep, and so I am not sure where to start looking for the problem.
Any idea why this is happening?
Thank you very much
Hi,
It would help if you could provide:
- Your version of fMRIprep
- How you are running it (singularity vs docker vs python)
- What flags were passed into fmriprep (or just share your full command if you are comfortable with that)
Thanks,
Steven
Hi Steven,
Thank you so much for your help.
- I use fMRIprep 20.2.3
- I am running it in singularity on a HPC
- These were the flags and commands passed into fmriprep:
subj=$1
module load singularity
echo “Running fMRIPrep on participant $subj”
singularity exec -e \
/rigel/psych/users/elfk/fmriprep_20.2.3.sif fmriprep \
/ \
/ \
–fs-license-file //license.text \
participant \
–participant_label $subj \
-t cond2 \
–skip-bids-validation \
–fd-spike-threshold 0.9 \
–nthreads 10 \
–random-seed 24 \
#for now don’t use freesurfer
–fs-no-reconall \
–ignore fieldmaps \
–output-spaces MNI152NLin2009cAsym:res-2 \
–cifti-output \
–force-bbr \
–skull-strip-template OASIS30ANTs \
–skull-strip-t1w force \
–stop-on-first-crash \
–notrack \
–work-dir work_nofreesurfer \
Hello,
A few suggestions:
Try upgrading to 21.0.1 or 20.2.7
If you ultimately want to use BBR, you will get better performance with Freesurfer outputs. I personally would not explicitly --force-bbr, especially when not using freesurfer.
Steven
Dear Steven,
Thank you so much for the help. In the last few days I have tried to follow your suggestions. I have upgraded the fmriprep version to 21.0.1, and also tried to run the script with or without the force-bbr command. Strangely, now, the script doesn’t work at all (and it did before). Specifically, I get the error: “fmriprep: error: unrecognized arguments:” and “command not found” for the following flags:
–skip-bids-validation
–nthreads
–output spaces
–skull strip template
I am attaching the script again in case I have accidentally changed more than I intended. Do you have any idea what may have caused this problem?
Thank you very much again,
Lior
subj=$1
module load singularity
echo “Running fMRIPrep on participant $subj at cond1”
singularity exec -e \
//fmriprep_21.0.1.sif fmriprep \
//bids/ \
//derivatives/01_fmriprep/ \
–fs-license-file //license.txt \
participant \
–participant_label $subj \
-t cond1 \
–skip-bids-validation \
–fd-spike-threshold 0.9 \
#–bids-filter-file fmriprep_preproc_cond1_run1.json
–nthreads 10 \
–random-seed 24 \
–fs-no-reconall \
–fs-license-file //license.txt \
–ignore fieldmaps \
–output-spaces MNI152NLin2009cAsym:res-2 \
–cifti-output \
–force-bbr \
–skull-strip-template OASIS30ANTs \
–skull-strip-t1w force \
–stop-on-first-crash \
–notrack \
–work-dir work_nofreesurfer \
I am guessing what is happening is that there is an accidental new line before those flags, so it is being parsed as separate commands instead of arguments to fMRIPrep.
You can change this to singularity run -e //fmriprep_21.0.1.sif since fmriprep is the default run command for the container.
I personally would not --force-bbr, especially if also doing --fs-no-reconall
This is the default behavior so you do not need to specify this
To be safe, I would use the absolute paths to all directories, instead of relative. This is just my personal preference, but it is usually easier to debug.
If you could attach precisely what the error message was, I think that would help.
Best,
Steven