Bruce, In that case, is there a way to have freesurfer output average cortical thickness throughout the entire cortex? In terms of total volumes, I noticed measures labeled IntraCranialVol and BrainSegVol in the wmparc and aseg stats files. I assume intracranial volume includes everything, even non-cortical regions? If that is so, is BrainSegVol a measure of total cortical volume? I also noticed that the values in BrainSegVol differ greatly between the two stats files. Your help is greatly appreciated,
Nathan -----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wed 3/11/2009 12:47 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aparcstats question Hi Nathan, the "unknown" label is intended to be non-cortical regions such as the callosum, and should be ignord. I think total white matter volume is generated by default, but maybe Nick or Doug can correct me (although Nick is out of the country) Bruce On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote: > Hello all, I sent this a couple of weeks ago but it must have slipped through > the cracks: > > I have a couple of questions regarding the stats files. First, at the > beginning of the aparc.stats tables, there is a measure that is labeled > ³unknown.² Is this total average thickness throughout the cortex, or just > some throw-away measure? > > Secondly, I have heard that there are command line flags that can be used to > find things such as total white matter volume, etc. What are these flags? > Thank you in advance, > > Nathan > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
