Summary of what happened:
We collect two multiecho resting state scans, the longer being the AP direction (~20 minutes) and the shorter in the PA (~10 minutes). Sifting through different conversations on here, I was able to test a few different ways of getting fmriprep to recognize the first echo of each as a field map. The way that finally worked was when I renamed the first echo of each run to sub-P###_ses-baseline_dir-AP_run-01_epi.nii.gz & sub-P###_ses-baseline_dir-PA_run-01_epi.nii.gz. I added an IntendedFor listing all fives echos + their sbref files in each direction to both of the jsons. I added a B0FieldIdentifier: sub-P### and a RawSources: to the fmap jsons + a B0FieldSource: sub-P### to each of the individual echo jsons.
Things seemed to run correctly because a fmap folder was produced, but the summary html lists: Susceptibility distortion correction: None
I was hoping someone could tell me why would fmap be produced but then ‘Susceptibility distortion correction: None’ would be in the html?
The output fmap folder contains:
sub-P###_ses-baseline_run-1_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
sub-P###_ses-baseline_run-1_fmapid-auto00000_desc-preproc_fieldmap.json
sub-P###_ses-baseline_run-1_fmapid-auto00000_desc-epi_fieldmap.nii.gz
sub-P###_ses-baseline_run-1_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
but in the output func folder there are no files related to auto00000.
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv \
--no-home \
-B ${jobTmpDir}:/tmp \
-B "/home/julgrier/templateflow:/templateflow" \
-B "/appl/freesurfer-7.1.1:/freesurfer" \
-B ${inputdir}:/data/input \
-B ${outputdir}:/data/output \
-B /project/fmriprep/prerun_output/$1:/fssubdir \
/project/singularity_containers/fmriprep-23.2.3.simg \
/data/input /data/output participant \
--skull-strip-template OASIS30ANTs \
--fs-license-file /freesurfer/license.txt \
--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 \
--me-output-echos \
--notrack \
--nthreads 16 --omp-nthreads 15 \
--work-dir ${SINGULARITYENV_TMPDIR} \
--skip_bids_validation \
--stop-on-first-crash \
--verbose \
--participant-label $1
Version:
fMRIPrep 23.2.3
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Relevant log outputs (up to 20 lines):
log:
fMRIPrep finished successfully!
html:
Susceptibility distortion correction: None
but then further down:
Alignment of functional and anatomical MRI data (coregistration)
This panel shows the alignment of the reference EPI (BOLD) image to the anatomical (T1-weighted) image. The reference EPI has been contrast enhanced and susceptibility-distortion corrected (if applicable) for improved anatomical fidelity. The anatomical image has been resampled into EPI space, as well as the anatomical white matter mask, which appears as a red contour.
