Suppose I were to open a subject aseg.mgz in tkmedit, and use the 3D fill tool to relabel the *entire* left hippocampus segmentation to 'MyNewImaginaryLabel'. If I then re-run the aseg stats, should the left hippocampus volume from the original aseg.stats be identical to the volume of MyImaginaryLabel in the newly generated aseg.stats?
Every voxel from the prior label is now assigned to the new label; yet, I am getting different results (by about 100 voxels in the ones I've tried).
The command Im using to recalculate: mri_segstats --seg /usr/local/freesurfer/subjects/s02/new_MRI/new/aseg.auto.mgz --sum /usr/local/freesurfer/subjects/s02/stats/NEWmethod1aseg_Hipp.stats --pv /usr/local/freesurfer/subjects/s02/mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask /usr/local/freesurfer/subjects/s02/mri/brainmask.mgz --in /usr/local/freesurfer/subjects/s02/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab /usr/local/freesurfer/8regions.txt --subject s02;
Now if I were to relabel 'MyNewImaginaryLabel' to 'AthirdLabel', and again changing every voxel in 'MyNewImaginaryLabel' to the new label, the computed volumes do not change. This led me to suspect that aseg.mgz contains probability estimates at each voxel that are then subsequently overwritten by my tkmedits. However, per a previous conversation from a year ago or so with Bruce and also the relevant Freesurfer documentation this does not seem to be the case. Partial volume information is not contained within the aseg.mgz (right!?), but is computed by mri_segstats by comparing border voxels with intensities in the norm.mgz. So I am at a loss on why these should be different.
This has been replicated in version 4.5 and 5.1 - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805