Hi Abby
if you load your original nifti do the directions display properly? That is, are right/anterior/superior as shown by freeview in the correct directions anatomically?
cheers Bruce
On Thu, 4 Apr 2019, Abby tang wrote:
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Hello FreeSurfer Developers,
I'm attempting to recon_all my subjects which is .nii file. But I usually meet this error.
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0 000 < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2019:04:04:10:30:25 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 50% M 6252 F 7 R 243 W 0 c 1 w 8 I 1384 O 0 L 1.11 0.48 0.21 @#@FSLOADPOST 2019:04:04:10:30:25 talairach_afd N 4 1.11 0.48 0.21 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 ERROR: Talairach failed! Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_6 4 x86_64 GNU/Linux recon-all -s 0306A_T1_w4 exited with ERRORS at Thu Apr 4 10:30:25 CST 2019 For more details, see the log file /home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4 /scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I've searched the list and they advised to check with this website https://surfer.nmr.mgh.harvard.ed u/fswiki/FsTutorial/Talairach_freeview. however,my subject's recon_all folder doesn't have T1.mgz a nd brainmask.mgz. it just has mri_nu_correct.mni.log orig orig_nu.mgz transforms mri_n u_correct.mni.log.bak orig.mgz rawavg.mgz
I run ten files, and almost all of them go wrong, which is very strange.I need your help. please giv e some advises with program statements in detail.
I really appreciate your help
- FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
- Platform: ubuntu 18
- recon-all.log:see attached