VBM with smriprep

Software Support
1

Summary of what happened:

Dear smriprep experts, I am running the script below to segment and normalize to MNI ~800 T1w volumes. I would like now to run a VBM analysis and I was wondering if I can use the *space-MNI152NLin2009aAsym_res-1_label-GM_probseg.nii.gz maps generated by smriprep.

  • Maybe I can use something like fslvbm_3_proc ? Because the data are processed with smriprep I didn’t run fslvbm_2_template, so I guess I don’t have its derivatives within smriprep outputs.

  • Is there a modulation of the warped voxels when running the normalization with smriprep?

Please let me know if you have any suggestion to run a VBM without having to re-process all the data.
Thank you,
F

Command used:

singularity run --cleanenv \
  --bind /data/imaging:/data/imaging \
  /data/imaging/data/softwares/smriprep-latest.simg \
  --output-spaces MNI152NLin2009aAsym:res-1 \
  -w /work_dir/smriprep/work \
  --notrack \
  --fast-track \
  -v \
  --fs-license-file /data/imaging/data/softwares/freesurfer/license.txt \
  /work_dir/bids/ \
  /work_dir/smriprep_out \
  participant \
  --participant-label ${SUBJECT}
2

Hi @fpizzagal,

Not a direct answer, but you can use the FreeSurfer files generated smriprep to run a surface based morphometry analysis (which in many ways could be preferable to VBM). You can run recon-all -s ${subject_id} -qcache to quickly generate fsaverage space morphometric maps at various levels of smoothing (after the free surfer subjects dir environmental variable is mapped to where your smriprep-derived freesurfer outputs are).

Best,
Steven

3

Thank you Steven, that is certainly an option.

I am interested in volumes measured from substructural areas, not extracted by freesurfer by default.
Do you know if I can extract volumetric info applying my custom atlas?

Best,
F

4

Hi @fpizzagal,

Would adding -subcortseg to the FreeSurfer command work for your purposes, to get these measurements? FreeSurferVersion3 - Free Surfer Wiki

Best,
Steven

5

Hi @Steven ,
I don’t think so, I have my own atlas to use. With a standard VBM (SPM or FSL like) I would use my atlas as a mask for running the stats.
Thanks,
F