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
