Hi Joshua
probabilities are computed internally, but not stored nor used in volume
calcualtions. Are you actually doing a 3D fill? I don't think the
hippocampus label is guaranteed to be connected. Can you try instead
replacing every voxel in matlab with the hippocampus index to your new one?
That I think should give you the same results.
cheers
Bruce
On Wed, 16 May 2012, Joshua Lee wrote:
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
