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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
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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
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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