Hi Jeff,
it is the talairach.xfm file you need to check. The wiki says http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV
To check the quality of the registration file talairach.xfm file:
cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk
Best, Martin
On Wed, 2011-05-04 at 08:20 -0400, Martin Reuter wrote:
Hi jeff. Probably your Talairach registrations fail. There are several different maps. I don't remember which one is the one used for the eTIV but it is documented on the wiki. You probably looked at the wrong transforms.
Best Martin
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On May 4, 2011, at 2:47 AM, Jeff Sadino jsadino.queens@gmail.com wrote:
Hello,
I asked a question similar to this last year when working with FS 4.3.1, and I'm hoping that there is something new in FS 5 that can help.
I am having a problem where a lot of my subjects' brains are larger than the eICV. In FS 4.3.1, it is happening in about 70/140 subjects, and in FS 5, it is happening in about 30/140 subjects. I checked them in tkregister2, and they look ok. I can use the --old-etiv-only command, but then the problem is that my ICV shoots up to 1.7L, and my brain/ICV ratio drops to .65, way to low to be reasonable. What could the reason for this be, and are there any other tricks that I could use?
Thank you, Jeff Sadino _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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