nipreps
fieldmap-less SDC in v. 23.2.0a2 producing odd/distorted results
What happened?
Version 23.2.0a2 of fMRIPrep is producing good-looking (non-distorted) susceptibility distortion corrected functional images for my dataset, when the SDC is based on acquired fieldmaps, which is great. But I've several subjects in this dataset for whom we don't have fieldmaps, so for them I tried the fieldmap-less SDC option (via the --use-syn-sdc option). Unfortunately this produced unusual-looking images, as shown in the attached files. (These are of my own brain, which I am happy to share.)
What command did you use?
cmd="${SINGULARITY_CMD} ${SING_BIDS_DIR} ${SING_BIDS_DIR}/${DERIVS_DIR} participant --participant-label $subject -w /work/ -vv --omp-nthreads 8 --nthreads 12 --mem_mb 30000 --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym --ignore slicetiming --skip-bids-validation --use-syn-sdc --fs-no-reconall"
What version of fMRIPrep are you running?
23.2.0a2
How are you running fMRIPrep?
Singularity
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
No response
Additional information / screenshots
No response
Yes, I thought this would come up. I've been focusing on the other methods to the exclusion of syn. I'm not positive I'll have time to track this down before the release. Possibly we should just disable it until we have time to fix it.
Hi @effigies, I also met the same problem as @atkinsonap with --use-syn-sdc option using fmriprep v. 23.2.0a2. The problem presents in the final image and in the "desc-coreg_boldref" image but NOT in the "desc-hmc_boldref" image. I think the problem is related to the fieldmap estimation from sdcflow.
