On 4/14/15 9:59 AM, Alshikho, Mohamad J. wrote:
Hi Doug,
If I check the file "aseg.stats" ( the output of the command line
recon-all –subjid –all ) I don't see in the table (in the file
"aseg.stats" ) any volumes regarding right and left hemispheric white
matter.
It is not supposed to be there. That measure is not as accurate as when
the surface is used. We prevent it from being reported in the aseg.stats
by running mri_segstats with --ctab ASegStatsLUT.txt which does not have
white mater in it. There are volumes in the aseg.stats file for lh and
rh white matter measured with the surface, but they are not in the
enumerated list, instead they are something like
# Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left
hemisphere cortical white matter volume, 237875.057850, mm^3
# Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right
hemisphere cortical white matter volume, 246435.219579, mm^3
# Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical
white matter volume, 484310.277429, mm^3
The mri_segstats in aseg.stats was reported as the following:
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent
--subcortgray --in mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
--totalgray --ctab /usr/local/freesurfer/stable5_1_0/ASegStatsLUT.txt
--subject 005101
I can generate the right and left hemispheric white matter in
"aseg.stats" If I repeat running the following command line (like what
was mentioned in FS wiki):
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg
--brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name
norm --in-intensity-units MR --etiv --subject 005101
My Questions are:
1.Which flag is responsible for showing/hiding the left and right
hemispheric white matter statistics from “aseg.stats”.
2.Why we have slight differences in the resultant volumes as an output
of the previous command lines.
3.Which command line do you recommend to generate the statistics.
4.Can I feed any additional flags to the command recon-all –subjid
–all in order to force mri_segstats to run like in the second
previous command line.
I am sorry for my long list of questions
Thanks in advance,
**Mohamad
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