Hi Sara, it looks like you are doing a functional constraint. See these slides

Hi FS group,

My goal is to calculate the % of voxels in a given region that are higher than a region-specific threshold. This is what I've done so far for each subject:

• recon T1
• coregister vol.nii to T1
• move aparc+aseg.mgz into functional space
• mri_segstats --i vol.nii --seg aparc+aseg.functionalspace.nii --sum vol.aparc+aseg.stats   to get NVoxels & mean stats
  

For each subject, for each cortical region (Seg1001-1035 & Seg2001-2035), I now want to count the number of voxels that are above region-specific thresholds as found in thresh.lst, ie.

  ctx-lh-bankssts    Seg1001    1.383697722
  ctx-lh-caudalanteriorcingulate    Seg1002    1.272858762
  ctx-lh-caudalmiddlefrontal    Seg1003    1.167540497
  ...

Do you have any advice on the best way to do this? I think I can use mri_segstats, but am not sure if I'm looking at the right arguments and/or if there is a more straightforward way to do this. This is what I have so far:

  foreach s (`cat s.lst`)   /   foreach seg (`cat thresh.lst | awk '{print $2}'`)

  set thresh = `cat thresh.lst | grep $seg | awk '{print $3}'`

  mri_segstats --i vol.nii --seg aparc+aseg.functionalspace.nii --id $seg --maskthresh $thresh --masksign pos --sum tmp.$seg.stats

  ...and then grep NVoxels from tmp.$seg.stats, grep total NVoxels from vol.aparc+aseg.stats, divide/echo into summary stats file?

Thank you in advance for any advice!

Best,

Sara

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer