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 <greve@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



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