PRIME-RE/prime-re.github.io

[Contact]: ribbon.mgz

johnerichards opened this issue · 6 comments

johnerichards commented

I have followed the pipeline on https://prime-re.github.io/structural/surfaces_and_flatmaps_notebook/Surfaces_and_Flatmaps.html. It was extremely helpful, thanks.

I am trying to create the gm ribbon on a subject, and the thickness. I used the makesurf to vol, and it asks for the ribbon.mgz. However, the ribbon was not created in the pipeline. Is there a "simple" way to create the ribbon? The code is below

Thanks, John

mri_surf2vol --subject fsSurf --o thickness-in-volume.nii.gz --so lh.white lh.thickness --so rh.white rh.thickness
Loading /work/jerlab/JERLab_MRI/S16001//fsSurf/mri/ribbon.mgz
error: mghRead(/work/jerlab/JERLab_MRI/S16001//fsSurf/mri/ribbon.mgz, -1): could not open file

pcklink commented

Hi John, I do not know from the top of my head, but I'd start with looking at the detailed table of (sub)procedures that are normally hidden in the recon-all pipeline for Freesurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. It specifies where and how certain outputs are generated. Hopefully it will put you on track to getting the robbon.mgz file.

johnerichards commented
johnerichards commented
pcklink commented

Hm, that sounds like a typical 'not-a-human-brain' problem indeed. I created the NHP-Freesurfer for surface visualisation and never used these steps. Perhaps the precon-all (https://github.com/neurabenn/precon_all) or PREEMACS (https://github.com/pGarciaS/PREEMACS) pipelines could be helpful?

johnerichards commented
pcklink commented

I find the AFNI developers extremely responsive and helpful, so that might be a good route.