Hi Martin (and others),

This worked! Great thanks. However, when I come to the skull-stripping sequence I get the message that WM values are lower than CSF. In some way this doesn't make sense, but when considering the T1.mgz file. It becomes clear from the segmentation it can be seen that the segmentation is somewhat off. But a large area takes values of around 110 and some of around 255. This odd segmentation can clearly be attributed to the template which is of course human. Is there a way of circumventing this issue? Or adjusting these values?

Thanks!

Mark

Martin Kavec wrote:

Mark,

without prior knowledge of what you do, I can just recommend you the recon-all option "-notal-check". You can find out more about it by running "recon-all -help | less".

So your command would look like:

recon-all -autorecon1 -notal-check -s $YOURRAT

Best,

Martin

On Monday 13 October 2008 12:29:52 Mark Bouts wrote:

...

Hi,

I'm trying to create a template model for rats. I've learned through the surface registration template (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) that I have to run the recon-all procedure at least once. However when I run the recon-all -autorecon1 option it stops at the the talairach detection after completing the talairach_avi. With the message:

Talairach Failure Detection

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)

I read through different messages on the mailing list that I had to check the nu.mgz file with tkmedit. This file looks ok considering the fact that a rat brain is considerably smaller.

So my question I like to ask is: how to continue? What could I try?

Is there a template available or does anyone have experience with creating a template for a rat?

Thanks!

Mark _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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