Hi Osei, Check out this wiki page for how to check the talairach transform and fix it if necessary. If everything looks decent then you can use the -notal-check flag to bypass this step in recon-all.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
-Louis
On Thu, 13 Feb 2014, Boadu, Osei B wrote:
Hello all, I am trying to do a reconstruction but I keep getting the following error (taken from recon-all.log):
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string.
Any help would be greatly appreciated and I attached the entire error log. Thank you!
Osei
The command line executed was: recon-all -all -subjid LCS13
Here is more pertinent information:
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
RedHat release: CentOS release 6.5 (Final)
Kernel info: Linux 2.6.32-431.1.2.0.1.el6.x86_64 x86_64
NMR Center info (/space/freesurfer exists):
machine: huygens
SUBJECTS_DIR: /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI
PWD: /homes/1/oboadu
ssh huygens setenv SUBJECTS_DIR /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI cd /homes/1/oboadu