External Email - Use Caution Dear Bruce, Martin, and experts,
I posted an issue a few days ago. I have been looking through the archives but can not figure out the solution myself. I was wondering if you would have any suggestion on how to fix the issue described further down? Thank you very much in advance Dani ---- Daniel Ferreira <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Daniel+Ferreira%22> Wed, 09 Jan 2019 10:22:05 -0800 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20190109> External Email - Use Caution Dear experts, I am processing some data and one of my cases failed. I checked the recon-all.log and found the following: *#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET* */home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/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)* *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.* *See:* *http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>* *ERROR: Talairach failed!* *Linux siv 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux* *recon-all -s 0e63e2e7-d1e1-4e78-9106-150994a32c44 exited with ERRORS at tis 11 dec 2018 11:32:31 CET* Next, I tried to fix the issue by using tkregister: tkregister2 --mgz --s tal_before --fstal However, the Talairach volume does not load as a MOVEABLE volume. When I check the available recon-all output I only have: orig/001 --> looks good rawavg --> looks good orig --> its awful (it looks like millions of white tiny voxels on a black background) nu --> it is empty transforms/talairach.xfm --> is available I was wondering if you would know about any way to fix this? Thank you in advance, Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padi...@ki.se <daniel.ferreira.padi...@ki.se>*
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