hmmm, that is convincing. I don't think there's anything in mri_segstats
that knows about the meaning of any of the indices, but maybe Doug can
correct me?
On Wed, 16 May 2012, Joshua Lee wrote:
Hi Bruce,
First, let me add that if I run the mri_segstats without the --pv flag, the
two will have identical volumes. This indicates to me that we captured all
the voxels into the new label.
Joshua
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
On Wed, May 16, 2012 at 1:38 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
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
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