External Email - Use Caution
Thanks for your reply! The command is:
tkregisterfv --s participant_name --fstal
ERROR: cannot find participant_name/surf/lh.white
Best
Stefan
________________________________
Von: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Douglas N. Greve
<dgr...@mgh.harvard.edu>
Gesendet: Donnerstag, 21. April 2022 20:03:32
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] ERROR: Talairach failed!
Can you provide the tkregisterfv command line and the terminal output?
On 4/21/2022 3:37 AM, Fritze, Stefan wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to compute recon-all -all -subjid XXX -qcache -3T, which works
fine with most of my study participants, but for some of them I receive
Talairach error (s. error message below):
I've searched the list and similar errors have been reported and there is a
webpage dealing with this type of error (MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to be
https://secure-web.cisco.com/1nJqbXyvi0ZdnVubukLDfIIP6F5eP0uDJmJ85ZEE2-CfZyDP7fKdoHGk-l9icpFIAJlrAGT-PQ6Yk7_Kyne4FQ4g9kjxgcAsKFfqoahpUZj_STuGENyfXk_MhQNUM6KlGj2vQ_Nj8J9MNgEDQOG7b_avUc_Qx20yIWfgbmUSQMJJ7vF5mXJ4dH3uENAGs-NhjmNRvuoLo9pWEPCE_bS3nk8cq37eSNo3-3NAoQxf4CyXge3ZHd_tprndBtwoyMGu1QzgXkAoGpU1liYZC93alD87NWvE04tppkYrkQbTelT6KjW5Yb9WD8mfkBFg0TB0DRTH2598UNIfee2yunY8wOQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach_freeview<https://secure-web.cisco.com/12PSM0kyIYIR5OmViKurKErWOjGNautv6OLjOZ2Xfwd9-oX2biUAK1AqD22LlXvKLAl5W6fybm9dLhz4luX4Eqiz2b0aS2ToqMmXx0qSLpx275tpw3qoUg_7fUXcZCCEp2RQpUERty8Yo6YaF6_Jtpqn5lyc7YK5ococ-pt2nmnkO-uvv0v7cCCl4i9XyLH9APKbI9tXzGzLhWXK9wDz13HbNxSYe3TtS7uSmGatyz5D7NUKn7BHK3a1blPd021yAJDL2u8jwgb1was-7uvCOhIhp1H6mAi-skh_cw0ETN2FlQZNqlcgOcQhZ5ZedSvE-tFtEYfcOTySxW1Mz8AXduQ/https%3A%2F%2Fsmex-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252fsecure%252dweb.cisco.com%252f1RvZhQl7xG9ZOQtDHxIejsIaxH%252dSzi0GVQwXNg3elCyaJxdS%255fia2rbovg7amDfXBOXgvzkzgRGIifK5a14I9S%252dY2wfUx%252dTyK5HpLSKuxchVxsveJhVmkXUABKfpKz3g1xPOw7DH9%255fRarrJdByWjKpp4O7t5mo2Ayi2KsghGio%252dQnbuEbUci21Tl4uEi%252dtGkDN1Hxd143cydV9CFXuRGWf1lB1Qe2YPkOJ4zNkRewkk1i%252dS%252df%255faGd9i%255f5RoGUgkY5lD1%252dh2rod%252d383tXpTQ%252dcZUsk%252dKAGAL0fHL8hh91V%255fVFMqQr%255flBuayIOjsP%255fFdc9aI2n1wlnbmr7zuzQtyDXVTvQ%252fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FFsTutorial%25252FTalairach%255ffreeview%26umid%3D7ed17774-f51c-4368-becd-51a015929d02%26auth%3D9ed9a254ae8a0a504cee5b89eb68d1de87cd0c46-65a702a50662ca1b466b6e9af5fe2bdc80c230ed>).
Yet, tkregisterfv produces also an error, even when I do not set the --surf
orig flag (the surf folder of these participants is empty). Running the
mritotal utility from the MNI toolset produces the same error. In one
participant, the problem was solved when I converted the .nifti file to .mgz
and started recon-all from there. But this did not help with the other
participants. Including the -notal-check flag allows recon-all to complete, yet
I do not know whether the results are trustworthy.
Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive
attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
2) Platform: 54G7T63 Kernel: 5.0.0-32-generic x86_64 bits: 64 compiler: gcc v:
7.4.0
Desktop: MATE 1.22.2 wm: marco dm: LightDM Distro: Linux Mint 19.3
Tricia
base: Ubuntu 18.04 bionic
3) recon-all.log: see attached
Best wishes,
Stefan
#@# Talairach Failure Detection Fr 11. Mär 18:44:03 CET 2022
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0321, pval=0.0034 < threshold=0.0050)
Command exited with non-zero status 1
@#@FSTIME 2022:03:11:18:44:03 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M
6312 F 0 R 247 W 0 c 0 w 1 I 0 O 0 L 83 1 60
@#@FSLOADPOST 2022:03:11:18:44:03 talairach_afd N 4 83 1 60
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/1UT1AAFsldR3wkUATYIjEYL_5proRYQNSNGyTJKVNntV131q733BTrj2ERp9j1sx_ZTmJ6m1ii08-Jornf4UaZNtx9z9STWU66ab0ZRezNjfHjPhkBk8Mkpll5hNSn7e02TvDumOnQQ867uveSad9BEooMLIIyw9oYxyu3bKPlLS6Qh-fMelrcPkwl_VGOtELnh0YKzS0zzfgOCvcW-xElF6BOF7hzl3qJkcqQoMGpdMGz8AvnD8n7umQcDySzH-0eE0uRorgYBBrc_K_Lh8M6VwpwdiqiC5L25pAIpaZw-CdK_fZlMr2xFlZa4LwttfvrbaiIURH0Pix3n0Uc3Ysmw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach
ERROR: Talairach failed!
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