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=0.0000 < 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_64 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.edu/fswiki/FsTutorial/Talairach_freeview. however,my subject's recon_all folder doesn't have T1.mgz and brainmask.mgz. it just has mri_nu_correct.mni.log orig orig_nu.mgz transforms mri_nu_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 give 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
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
- FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz
- Platform: ubuntu 18
- recon-all.log:see attached
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 CautionHello 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
External Email - Use Caution
Hi Bruce： I changed rawavg.mgz that picture attached below and rerun the subject. Unfortunately, the error did not change. I don't know the reason. Could you help me? I will appreciate your assistant. Abby
Bruce Fischl fischl@nmr.mgh.harvard.edu 于2019年4月5日周五 下午10:14写道：
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 CautionI 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 displayproperly? 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. ButI 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 U0.00 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 0.480.21
> 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 WedFeb 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 410:30:25 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, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > I've searched the list and they advised to check with thiswebsite
https://surfer.nmr.mgh.harvard.ed > u/fswiki/FsTutorial/Talairach_freeview. however,my subject'srecon_all folder doesn't
have T1.mgz a > nd brainmask.mgz. it just has mri_nu_correct.mni.log origorig_nu.mgztransforms mri_n > u_correct.mni.log.bak orig.mgz rawavg.mgz > > I run ten files, and almost all of them go wrong, which is verystrange.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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Abby tang -
Bruce Fischl