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Hi FreeSurfer Developers,
For our study we had to manually correct some recon-all outputs due to some
ROIs underestimation. For the purpose we manually edited the aparc+aseg.mgz
file using the "voxel edit” command from Freeview. Then we use the mri_segstats
command to extract volumes from the corrected aparc+aseg.mgz file. However,
from the MRI_segstats we didn’t obtain a new TIV value. I want to ask if the
TIV value is computed using the parcellation files (like aseg+aparc one) or
instead using the brain.mgz file. How can I check that the TIV value reported
in aseg.stats was unaffected from the underestimation we had to correct?
Please find below the command we use to compute volumes from the corrected
aseg+aparc file:
mri_segstats --seed 1234 --seg
/Applications/freesurfer/7.1.1/subjects/CorrectedSegmentations/${subj_id}.mgz
--sum /Applications/freesurfer/7.1.1/subjects/${subj_id}/stats/AllVolumes.stats
--pv /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz --empty
--brainmask
/Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/brainmask.mgz
--brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray
--in /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
--surf-ctx-vol --totalgray --euler --ctab
/Applications/freesurfer/7.1.1/AreasList.txt --subject ${subj_id}
Thank you for your support!
Daniela
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