Not sure about 1 and 3, but for 2 you'll probably want the new version of mri_segstats:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats
I've added a measure (BrainSegNotVent) which you will probably want to use. I've also added the text below to the --help.
doug
MEASURES OF BRAIN VOLUME
There will be three measures of brain volume in the output summary file: (1) BrainSegNotVent - sum of the volume of the structures identified in the aseg.mgz volume this will include cerebellum but not ventricles, CSF and dura. Includes partial volume compensation with --pv. This is probably the number you want to report. (2) BrainMask - total volume of non-zero voxels in brainmask.mgz. This will include cerebellum, ventricles, and possibly dura. This is probably not what you want to report. (3) BrainSeg - sum of the volume of the structures identified in the aseg.mgz volume. This will include cerebellum and ventricles but should exclude dura. This does not include partial volume compensation, so this number might be different than the sum of the segmentation volumes. (4) IntraCranialVol (ICV) - estimate of the intracranial volume based on the talairach transform. See surfer.nmr.mgh.harvard.edu/fswiki/eTIV for more details. This is the same measure as Estimated Total Intracranial Volume (eTIV).
Raznahan, Armin wrote:
Dear FreeSurfers
I am new to FreeSurfer, and to this Wiki. I am working in SPSS with measures from FreeSurfer sent to me by a collaborator. It would be great if anyone could help with the following..
- When I summate GrayVolume measures for each of the 35 regions in each
lobe, the total I get is about 50,000 less than that given under the automatically generated measure "CerebralCortex_Volume" for that lobe. I would be very grateful if someone could shed some light on this for me..
- Also - would anyone have advice on which of the three measures ;
Brain Mask Volume, Brain Segmentation Volume, and Intracranial Volume performs best as an index of total brain volume when one wants to address this as a covariate in analyses?
- Finally, I wondered if someone could confirm that the method for
calculating Gyrification Index in FreeSurfer is that which appears as formula #2 on the second page of VanEssen's 1997 paper "Structural and functional analyses of human cerebral cortex using a surface-based atlas. J Neurosci. Sep 15;17(18):7079-102". Does this formula produce an index of gyrification that reflects the gyrification of an given area in a manner not influenced by changes in the perimeter of the area in question ie would the GI for a cortical region with an even degree of gyrification "g" and "footprint" area "f" be the same as that which would be generated by the equation if the area were increased to "2f"?
All the best
Armin
Dr Armin Raznahan MBBS(Hons) MRCPCH MRCPsych Clinical Research Worker Institute of Psychiatry Department of Child and Adolescent Psychiatry PO85 16 De Crespigny Park London, SE5 8AF Tel: +44 (0)20 7848 0651 Fax: +44 (0)20 7708 5800 Email: armin.raznahan@iop.kcl.ac.uk
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