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 > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer