Hi All,
I would like the following precomputed files to be used by fmriprep instead of it re-running the below steps
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Skull-stripped mask
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My own 3 tissue type mask for 7T anatomical processing instead of FSL FAST since it does not do a good job of separating GM-WM for 7T MP2RAGE. When I placed the *dseg.nii.gz and *probseg.nii.gz labels in the anat derivative folder it would replace the current files during the run.
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And I would also like to use the freesurfer 8.0 output instead of 7.3 and in order to use precomputed output for downstream processing, can I use this flag “–fs-no-resume”? after placing the freesurfer output in */sourcedata/freesurfer/$subj/? At this point fsaverage files are not created.
Command
apptainer run \
-B /home/naxos2-raid14/jayashre/.cache/templateflow:/templateflow:ro \
-B /home/udall-raid5/bids-data/Control_data/Nifti:/data \
-B /home/udall-raid5/bids-data/Control_data/fmriprep/output_ses02:/output \
-B /home/udall-raid5/bids-data/Control_data/fmriprep/work_ses02:/work \
-B /opt/local/dbs/bin/license.txt:/license.txt:ro /opt/local/dbs/bin/fmriprep-latest.simg \
/data /output participant \
--participant-label C126 \
--session-label 02 \
-w /work \
--fs-license-file /license.txt \
--ignore slicetiming \
--skull-strip-t1w skip \
--output-spaces MNI152NLin2009cAsym:res-native T1w fsnative \
--nthreads 8 --omp-nthreads 6 \
--skip-bids-validation
Version:
fmriprep 25.2.3
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer
OS: Linux Ubuntu 22.04.5