Summary of what happened:
Hi all,
I am having an issue with the automatic bold-to-T1 registration coming out fairly significantly misaligned for the functional data that I am trying to analyze. This is causing some downstream issues with group analysis, so I’m looking for a solution that is reasonable for a large dataset.
Command used (and if a helper script was used, a link to the helper script or the command generated):
inputdir=/project/oathes_analysis2/R61/bids
outputdir=/project/oathes_analysis2/R61/fmriprep/prerun_output/$1
singularity run --cleanenv \
--no-home \
-B ${jobTmpDir}:/tmp \
-B "/project/oathes_analysis2/templateflow:/templateflow" \
-B "/appl/freesurfer-7.1.1:/freesurfer" \
-B ${inputdir}:/data/input \
-B ${outputdir}:/data/output \
-B /project/oathes_analysis2/R61/fmriprep/prerun_output/$1:/fssubdir \
-B /project/oathes_analysis2/R61:/basepath \
/project/oathes_analysis2/singularity_containers/fmriprep-23.2.3.simg \
/data/input /data/output participant --skull-strip-template OASIS30ANTs --fs-license-file /freesurfer/license.txt \
--bids-filter-file /basepath/bids_filter_file_tmsfmri.json \
--fs-subjects-dir /fssubdir/sourcedata/freesurfer \
--output-spaces T1w MNI152NLin6Asym:res-2 \
--bold2t1w-dof 6 \
--dvars-spike-threshold 1.5 \
--fd-spike-threshold 0.5 \
--ignore slicetiming \
--notrack --nthreads 16 --omp-nthreads 15 --work-dir ${SINGULARITYENV_TMPDIR} --verbose --participant-label $1
Version:
fmriprep-23.2.3
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity/Apptainer
Screenshots / relevant information:
We are using a reverse phase encode direction image (dir-PA_epi) for fieldmap correction, using the “IntendedFor” json field.
This image shows the “original” BOLD image before any T1 alignment, and as you can see it’s pretty far from the T1’s FOV, but not terribly crooked or rotated, so I expected the registration to turn out better than it has.
Any recommendations are very welcome. I’ve read through many other posts and tried alternative options with the
--force_no_bbr and --bold2t1w-dof flags in the fmriprep call, with no change.