Full freesurfer longitudinal output

[butellyn]

What would you like to see added in fMRIPrep?

I've noticed that when I run fmriprep with the --longitudinal flag, it does not include the individual session structural output from freesurfer. My understanding is that the freesurfer longitudinal pipeline runs the full cross-sectional pipeline on all sessions, and creates an unbiased single subject template. I also don't see much freesurfer output at all. Does fmriprep clean out most of the freesurfer output when you run it with the --longitudinal flag? It would be nice to have all of it. Below is my call, and my general output:

SINGULARITYENV_TEMPLATEFLOW_HOME=/home/fmriprep/.cache/templateflow \
     singularity run --writable-tmpfs --cleanenv --containall \
     -B /tmp:/tmp -B /projects/b1108:/projects/b1108 \
     -B /projects/b1108/software/freesurfer_license/license.txt:/opt/freesurfer/license.txt \
     -B /projects/b1108/templateflow:/home/fmriprep/.cache/templateflow \ 
     /projects/b1108/software/singularity_images/fmriprep_21.0.2.sif \ 
     /projects/b1108/studies/mwmh/data/raw/neuroimaging/bids/ \
     /projects/b1108/studies/mwmh/data/processed/neuroimaging/fmriprep/ participant --participant-label MWMH352 \
     --longitudinal --nprocs=1 --omp-nthreads=1 \
     -w /projects/b1108/studies/mwmh/data/processed/neuroimaging/work2 \
     --fs-license-file /opt/freesurfer/license.txt --output-spaces MNI152NLin6Asym \
     --skull-strip-template OASIS30ANTs

Output:

Do you have any interest in helping implement the feature?

Yes, but I would need guidance

Additional information / screenshots

No response

[effigies]

Missed this when coming back from summer vacation, apologies. I think this is going to be possible in the near future with nipy/nipype#3529. We will need assistance from somebody familiar with FreeSurfer longitudinal to implement it, however.

[effigies]

Further discussion should take place in nipreps/smriprep#21.