and the papers describing the subcortical segmentation scheme are found at the bottom of the main wiki page:
http://surfer.nmr.mgh.harvard.edu/fswiki in the section 'subcortical segmentation'. On Tue, 2007-11-13 at 15:17 -0500, Doug Greve wrote: > Look in $FREESURFER_HOME/FreeSurferColorLUT.txt > > doug > > joel bruss wrote: > > This is the last question that I have...sorry to keep bothering you > > all. Is there a page on the FS wiki or is there a man page that > > details the value of each sub-cortical parcel? I see that each masked > > are has a value (1, 2, 3, etc.) but before I make assumptions about > > which values correspond with which region, I though I'd ask for help. > > > > -Joel > > > > On Nov 13, 2007 1:09 PM, Bruce Fischl <[EMAIL PROTECTED]> wrote: > > > > > Hi Joel, > > > > > > both the .m3z (nonlinear) and the .lta (linear) are transforms from the > > > subject to the atlas coordinate system, but all the labeling is done in > > > the subject space, so you should be set. > > > > > > cheers, > > > Bruce > > > On Tue, 13 Nov 2007, joel bruss > > > wrote: > > > > > > > > > > > > > Hello- > > > > > > > > I'm running FreeSurfer v4.01on SUSE Linux > > > > > > > > I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but > > > > in the native MRI space. I see that the output of "CA Label" produces > > > > a file that is fit to the "CA Normalize" step but I can't figure out > > > > the transform that was used. Specifically, for CA Normalize, if I > > > > look under /mri/transforms, and sort by time, I have both the > > > > talairach.lta and talairach.m3z files, but neither will get me from > > > > native to norm space (or vice-versa). Is there a transform file that > > > > I'm missing or is this a process of intermediate steps to get from > > > > native to norm space? Please help! > > > > > > > > Thanks, > > > > Joel > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://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 > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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
