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:

>
>         External Email - Use Caution        
>
> 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
>
> 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
> 2) Platform: ubuntu 18
> 3) recon-all.log:see attached
>
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