Hi Doug, My system is Linux Centos 7 I tried to run it and I got:
[malshikh@glia 002201]$ 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 --seg-erode 2 --ctab /usr/local/freesurfer/stable5_1_0/ASegStatsLUT.txt --subject 002201 ERROR: Option --seg-erode unknown ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, April 13, 2015 3:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats flags Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats This is for linux. If that is not your system, tell me what your system is doug On 04/13/2015 02:22 PM, Alshikho, Mohamad J. wrote: > > Hi Doug, > > Kindly I have the following questions regarding the command mri_segstats: > > ·I wanted to use the flag --seg-erode 2 in the command mri_segstats > but I am receiving an error message that this flag is not available ( > I am using FreeSurfer 5.3.0 ). > > ·When the command recon-all finish. I don’t see the right or left > cerebral white matter volumes in “aseg.stats”. Do I need to use > specific flags in order to generate the statistics related to left and > right hemispheric white matter. My command is like this: > > 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 075801 > > Bests, > > Mohamad > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
