If you have 5.3 installed, you can just run mri_segstats --seg mri/aseg.mgz --sum stats/aseg.v53.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --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 --euler --ctab /usr/local/freesurfer/stable5/ASegStatsLUT.txt --subject subjectname
this will only create a new stats file (aseg.v53.stats). If you just want to replace the one that is there, then spec aseg.stats instead of aseg.v53.stats doug On 06/03/2013 05:54 PM, Derek James Dean wrote: > Hello, > > I am a novice, working with aseg.stats data that were processed using > Freesurfer 5.1. A colleague requested a measure of total brain volume > that does not include CSF for each subject. My understanding is that > Freesurfer 5.2 and new versions provide BrainSegNotVent, which seems > like the best measure for what my colleague requested. Is there a way > to compute the BrainSegNotVent value with the Freesurfer 5.1 processed > data? Do I need to re-run recon all with Freesurfer 5.3? Is there > another way to get a total brain matter volume measure not including CSF? > > Thank you in advance for your help with this question. > > Best, > > Derek Dean > University of Colorado at Boulder > Dept. of Psychology and Neuroscience > > > > > _______________________________________________ > 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 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.
