Hi Abby

if you upload an image that fails we will take a look. If I had to guess,
I would say it is because you have so much non-brain tissue (neck and even
shoulders). YOu could try cropping your rawavg.mgz with the freeview
tools->crop tool to elimate stuff below brainstem and see if that helps
cheers
Bruce


On Fri, 5 Apr 2019, Abby tang wrote:

>
>         External Email - Use Caution        
>
> I load my original nifti through freeview and they are right directions display. 
> I attached two picture which are different subjects with letter. one of them,called
> correct,processed as normal. Another is the subject with problem as mentioned.
> I hope you can give me some other advises.Thank you so much.
>
> Bruce Fischl <fischl@nmr.mgh.harvard.edu> 于2019年4月4日周四 下午9:42写道：
>       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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>
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