Thanks very much Doug, I'll use this method. In case it helps anyone else, the "--supertent" option in the command provided should probably be "supratent".
Tom On Mon, Apr 25, 2011 at 3:44 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>wrote: > Here are two that were suggested by anothers on the FS list: > > Winkler AM, Kochunov P, Blangero J, Almasy L, Zilles K, Fox PT, > Duggirala R, Glahn DC. Cortical thickness or grey matter volume? The > importance of selecting the phenotype for imaging genetics studies. > Neuroimage. 2010 Nov > 15;53(3):1135-46.http://www.ncbi.nlm.nih.gov/pubmed/20006715 > > > Cerasa et al., Dysbindin C-A-T haplotype is associated with > thicker medial orbitofrontal cortex in healthy population. Neuroimage 2011 > > You might also look at Voets, Hough et al., 2008 > > As for your other question, it's been a while since I looked at a 4.2 stats > file. There are some things that look wrong in the steps that you have given. > The aseg.stats file from 4.2 should have had something in the header to > indicate the total white matter volume. Probably the easiest thing to do is > to run the version 5 mri_segstats program on your version 4.2 data, something > like: > > > cd $SUBJECTS_DIR/yoursubject > > mri_segstats --seg mri/aseg.mgz --sum stats/new.aseg.stats --pv > mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supertent --subcortgray > --totalgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units > MR --etiv --surf-wm-vol --surf-ctx-vol --ctab > $FREESURFER_HOME/ASegStatsLUT.txt --subject yoursubject > > This will create "new.aseg.stats". In the header of this file you will find > Total Gray and Total White volume measures. > > doug > > > > On 4/25/11 12:44 PM, Thomas Ballinger wrote: > > Hello, > I've been asked to obtain freesurfer volume measurements on some cases > we've already run with Freesurfer for comparison to VBM measurements. Can > anyone direct me to any literature or briefly share knowledge about > comparing these two methods? > > Second question: > For said analysis, I'd like to get the total white and grey matter volume > from the Freesurfer cases. The cases were run with Freesurfer 4.2, so I > don't have access to some of the tools I'm found referenced in discussions > of finding total grey matter in the mailing list archives. How does this > look for a total grey matter method? somewhat taken from > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10468.html > > 1. Get total supratentorial (i.e. sans cerebellum) WM+GM volume. > ("BrainSegVolNotVent" in wmparc.stats) > 2. Get cerebral WM volume. (wmparc.stats reports the value of total > cerebral white matter volume) > 3. Subtract 2 from 1 to get total supratentorial GM volume. > 4. Get whole brain GM and WM volumes by adding in cerebellar > volumes.(wmparc.stats L/R Cerebellum WM/Cortex) > 5. Calculate total CSF volumes by summing the individual ventricle and > "other" CSF values.(calculate from aseg.stats or wmparc.stats by summing > *-Lateral-Ventricle, *-Inf-Lat-Vent, 3rd-Ventricle, 4th-Ventricle, CSF, and > 5th-Ventricle) > > Thanks very much to anyone with time to respond, > > Thomas Ballinger > Research Assistant at PNL at BWH > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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. > >
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