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
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
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
Send from my phone
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Jeff Sadino -
Martin Reuter