External Email - Use Caution
Hi, Freesurfer team
I have met a Talairach Failure problem when running the recon -all for a subject, here is the feedback: I tried -notal-check flag, but it might cause another problem when I use segmentHA_T2.sh to do hippocampus subfield segmentation. So, Could you help me to solve this problem? Thanks.
#-------------------------------------------- #@# Talairach Failure Detection Mon Dec 21 17:59:09 EST 2020 /scratch/weishao/20191017_BAY10224/sub-BAY10224_Negar/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) @#@FSTIME 2020:12:21:17:59:09 talairach_afd N 4 e 0.07 S 0.01 U 0.00 P 18% M 6672 F 0 R 2777 W 0 c 2 w 65 I 1504 O 0 L 12.75 18.35 27.51 @#@FSLOADPOST 2020:12:21:17:59:09 talairach_afd N 4 12.75 18.35 27.51
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://secure-web.cisco.com/1_6NU0uyplJn2Ny1P23HKLCy4v6xjIjGaWl1oZJY8FTyZ1fb...
ERROR: Talairach failed!
Linux gra824 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux
recon-all -s sub-BAY10224_Negar exited with ERRORS at Mon Dec 21 17:59:09 EST 2020
Best, Wei
:
That is just the failure detection. Sometimes it generates a false positive. Did you check the transform? If the rest of the downstream processes (eg, aseg and surfaces) are ok, then you don't need to worrry
On 12/21/2020 6:53 PM, Wei Shao wrote:
External Email - Use Caution
Hi, Freesurfer team
I have met a Talairach Failure problem when running the recon -all for a subject, here is the feedback: I tried -notal-check flag, but it might cause another problem when I use segmentHA_T2.sh to do hippocampus subfield segmentation. So, Could you help me to solve this problem? Thanks.
#-------------------------------------------- #@# Talairach Failure Detection Mon Dec 21 17:59:09 EST 2020 /scratch/weishao/20191017_BAY10224/sub-BAY10224_Negar/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) @#@FSTIME 2020:12:21:17:59:09 talairach_afd N 4 e 0.07 S 0.01 U 0.00 P 18% M 6672 F 0 R 2777 W 0 c 2 w 65 I 1504 O 0 L 12.75 18.35 27.51 @#@FSLOADPOST 2020:12:21:17:59:09 talairach_afd N 4 12.75 18.35 27.51
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:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairachhttp://secure-web.cisco.com/1_6NU0uyplJn2Ny1P23HKLCy4v6xjIjGaWl1oZJY8FTyZ1fbUcZRmKspBxJlynhFmyDvpB5zZydgw7W3SM9hfCGvOLgESAsRsl5GyKDdulFu6aduP94X2BwjqSgZuvL3d7rTq_jfDF4gvVTlEB-H2_0of1E2u0x2DmzaMGFxXXlThHkPTCEUhRUm2Q3TfaGcYJ0vrvkyH1DlUbexb5LjdlaCyvOG8taQiQJdq2aAzbUFSkkOwqCCSRS4JeXLEiyjtfs-wjC9QWC_BlhloyUfmbw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach
ERROR: Talairach failed!
Linux gra824 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux
recon-all -s sub-BAY10224_Negar exited with ERRORS at Mon Dec 21 17:59:09 EST 2020
Best, Wei
:
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Greve, Douglas N.,Ph.D. -
Wei Shao