Hi Falk,

you can check the transforms via:

cd $SUBJECTS_DIR/$subject/mri mri_convert -rt nearest aseg.mgz -rl $FREESURFER_HOME/average/RB_all_2008-03-26.gca -at transforms/talairach.m3z aseg_in_atlas.mgz freeview -v aseg_in_atlas.mgz:colormap=lut /homes/4/fischl/dev/freesurfer/average/RB_all_2008-03-26.gca#1:colormap=lut

the mri_convert applies the nonlinear warp to the aseg and reslices it into the same voxel space as the atlas (you could use the talairach.lta to check it instead if you want, or apply it to the norm without the -rt nearest switch). Then freeview loads them both and you can switch back and forth with alt-c to see if they are in register. The #1 at the end of the gca means frame index 1, which is by convention the label with the highest prior at that location in the atlas (frame index 0 is the mean intensity of the most probably class).

cheers, Bruce

On Thu, 28 May 2009, Falk Lüsebrink wrote:

Hi Martin,

Thanks for the input, but I think you got me wrong. The talairach registration and talairach check during -autorecon1 is fine. I think the -careg stage during -autorecon2 might fail, which "generates a multi-dimensinal talairach transform" (mri_ca_register). And I was looking for something like the tutorials you mentioned, however not for the talairach registration during -autorecon1, but for mri_ca_register.

Regards, Falk

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Kavec Sent: Thursday, May 28, 2009 1:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Troubleshooting

Hi Falk,

On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote:

...

Hello,

I’m having trouble to generate a correct aseg.mgz for one volume of mine. The nu_noneck.mgz is also incorrect and therefore I think the -careg stage of autorecon2 might fail. Is there a way to do some kind quality check, like the tal-check during autorecon1, to see whether the talairach.m3z is incorrect? Are there some kind of instructions like fixing the bad output from the talairach registration?

For this you can follow instruction on

http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction

and more specifically

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

Hope some of that may lead you to successful reconstruction.

Best,

Martin

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