Summary of what happened:
Hello all,
I am interested in passing minimally preprocessed functional images as inputs to fmriprep and I’m wondering how to accomplish this?
Specifically, I would like to preregister the fMRI images to the preprocessed T1 in order to improve downstream analysis and registration using something like FSL epi_reg. For several of our subjects, the head was positioned at odd angles to accommodate our stimulus and fmriprep has not handled those cases super well.
I am using a prerun Freesurfer output for anatomical preprocessing, and all of my raw images are in bids format prior to running fmriprep. How would I include these preregistered images? Is there an appropriate bids format for manipulated images?
As an example, here is a raw image compared to the fmriprep preprocessing vs a quick epi_reg
Raw:
fmriprep:
epi_reg:
Essentially, I would like to use the epi_reg image as my fmriprep input rather than the raw image, but don’t know how to make that jive using the bids input format.
Thanks in advance.
Command used (and if a helper script was used, a link to the helper script or the command generated):
Here’s the fmriprep command that I’ve been using
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/individual_projects/jess/R61_tmsfmri_fmriprep_test:/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 fsaverage T1w fsnative fsLR MNI152NLin6Asym:res-2 --cifti-output 91k \
--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 via LPC bsub cluster