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.
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
_______________________________________________
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.
