we don't actually transform the data into tal coords - we just compute the transform for reporting (and a few computational) purposes.

cheers, Bruce On Wed, 16 Sep 2009, Fischi Gomez Elda wrote:

Hi all,

i'm trying to run only the -autorecon1 step of the cortical reconstruction process, but I don't want my data to be transformed into a Talairach template. As I've read on the Freesurfer wiki, I can remove any step of the process using the -no<step> flag, so in my case should be -notalairach.

I've tried both:

         recon-all -autorecon1 -notalairach  -subjid <subjid>

         recon-all -notalairach -autorecon1 -subjid <subjid>

and both exited with the same ERROR: "Tailarach failure detection"

###################################################################################################################

Wed Sep 16 12:34:37 CEST 2009 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Wed Sep 16 12:34:37 CEST 2009 /home/elda/freesurfer/subjects/Tamara/mri

talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Sep 16 12:34:37 CEST 2009

#######################################################################################################################

It means that is still trying to make compute the talairach transform that maps the input volume to the MNI average_305. ? What should I do to avoid this transformation?

Thanks

Elda Fischi Gómez

Ecole Polytechnique Fédérale de Lausanne (EPFL) Signal Processing Laboratories (LTS5) EPFL-STI-ITS-LTS5, ELD 224 (Bâtiment ELD) Station 11 CH-1015 Lausanne, Switzerland

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