Hires reconstruction not disabled - fmriprep 1.3.0


I’m trying to run the new version of fmriprep on my sub-millimiter anatomical data, but I want to disable the hires reconstruction. I’m running the following command:

singularity run -B /nfs/k_lab
/nfs/k_lab/data/SB-ref/anat_nosubmm/sourcedata /nfs/k_lab/data/SB-ref/anat_nosubmm/derivatives participant
–participant-label sub-$SJ_NR --output-space T1w template fsaverage6
–nthreads 15 --omp-nthreads 15 --low-mem --fs-license-file /home/inesv/freesurfer/license.txt
–no-submm-recon --anat-only -w /scratch

However my processed data still comes out with 0.64x0.64x0.64mm…
Not sure why this is happening, has anyone experienced the same with this new version?


Hi @ines

Thank you for your question. The --no-submm-recon call doesn’t change the voxel size of the anatomical image. This only means that the FreeSurfer T1.mgz is resampled to 1mm^3.

By chance, are you re-using an existing FreeSurfer directory that was previously run with -hires? In that case, the T1.mgz will still retain the original resolution. Deleting the FreeSurfer subject directory before running fMRIPrep should solve that case.

Hi Franklin,

Thanks for the reply. I noticed that only the Freesurfer T1w output was resampled to 1mm right after posting this here. So problem solved.


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