Re: [Freesurfer] [FreeSurfer] Process terminated when talairach was running

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Dear Douglas,

My apologies for the late reply as I have been trying to fix this issue and working on other things as well.

As I opened the 001.mgz file, I don't see any parts of brain being cut off, or any other strange things going on. For this particular subject, none of the surface files generated. I am not sure if I do it correctly. I opened 001.mgz with freeview, and find out that there is a "Transform Volume..." button under "Tools". Is that what you mean? If it is not correct, would you please kindly advice on how to run tkregisterfv with the tkregister 2 command line?

Thank you.

Best regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: 15 May 2023 21:48:10 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] Process terminated when talairach was running

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First, look at the volume for this subject (ie, subject/mri/orig/001.mgz). Is there anything strange about it? Artifacts? Part of the head/brain cut off? Pathology? If not, try to use freeview and not tkregsiter2. Actually, you can use tkregisterfv with the tkregister2 command line and it will run freeview in a way that you can view/edit the registration.

On 5/15/2023 5:19 AM, Krystal Xiwing Yau wrote:

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Dear FreeSurfer experts,

I tried to run on another pc in attempt to run recon-all without the previous error as mentioned. However, another error occurred, which is related to talairach as well. Below is the excerpt of which the attached error log recorded:

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2023:05:15:16:54:02 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 6652 F 0 R 261 W 0 c 0 w 1 I 0 O 0 L 3.05 2.96 2.78 @#@FSLOADPOST 2023:05:15:16:54:02 talairach_afd N 4 3.05 2.96 2.78

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://secure-web.cisco.com/1IeiO_eNx7hnB5PAYnz2mZs8gScM81SYQQ7rpk_lwHz-x90I...http://secure-web.cisco.com/1xBKhwqQkS_jkT7XbeZ1gFsqv6qNmlv33KPgMiuP7tsrBEYTq54OHtKgLcfgHc2er5HgGdvfoO1yTOwcffg8eXH6VqoVD_ap5A7aKxGyAVJnAKOLXMUG5Ti938jMwoqYkM8jdUd3FoIBaTi7Ty7GRTtgwwTJ57ccASjzTYI_oHh51bxLD9s7lFF3jprrnjVQO30pJQ8hAJhVCEykL3galYZgkKvDKGnDHc9a7Y2fCTyOZZj-eLbB6QKwWvb_o99AE/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach

ERROR: Talairach failed!

I followed the suggested webpage to fix the issue but failed. The wiki instructs us to move by left-clicking the slider below each plane. Unfortunately, I could only control the red cross on the window, while the target image was still not moveable...

[cid:part1.Av0CGbid.RsjBfQMH@mgh.harvard.edu]

Is there any way I can fix this error? Thank you very much.

Best,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Krystal Xiwing Yau krystaly@hku.hkmailto:krystaly@hku.hk Sent: 15 May 2023 10:36:20 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] Process terminated when talairach was running

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Dear Douglas,

It's on the HPC.

Regards,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Sent: 12 May 2023 21:37:21 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [FreeSurfer] Process terminated when talairach was running

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That's weird. In the echo below, is that from your shell or on the HCP? When you source the FS environment, that variable will be set.

On 5/12/2023 5:33 AM, Krystal Xiwing Yau wrote:

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Dear FreeSurfer expoerts,

I am running recon-all for the subject on a HPC. It exited with error when talairach was running - it indicated "MINC_BIN_DIR: Undefined variable". The log file is attached to this email.

I tried to look up the directory, which contains MINC_BIN_DIR as indicated on the https://secure-web.cisco.com/1Yi_rx3_ryx7Z_5U9Ro-U7Ztjy451lAhdmjzkMKbcgnaOryly22-jgU15upXMCDwhN7rCKUIx8fQlYSfQPlLd-pPd3G9E4tgLdtUGxIjQLS6io1g6lGqUeJV-4rJvteW_vA9dv9ct_wrIlMSVMMY1Wau7Ch4QiljAtc8p10M8CO1ECOvPp49pX9YUy6zgOlDa-FjJ8g7oFRFigjX9WLaJ8jXCp-XYml0EDexGHCBHRMt9QO64li3sTJKh4k2h7LAZkVb0Zb8BW6RTSHbzNVJSXEp-dLkCqpvbRrKtXQbX6ONS2t-I0Mva3GTfkdJm1Urd6fk2854W0ok7dIZ2WYtMcQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg01633.html forum https://secure-web.cisco.com/1Yi_rx3_ryx7Z_5U9Ro-U7Ztjy451lAhdmjzkMKbcgnaOryly22-jgU15upXMCDwhN7rCKUIx8fQlYSfQPlLd-pPd3G9E4tgLdtUGxIjQLS6io1g6lGqUeJV-4rJvteW_vA9dv9ct_wrIlMSVMMY1Wau7Ch4QiljAtc8p10M8CO1ECOvPp49pX9YUy6zgOlDa-FjJ8g7oFRFigjX9WLaJ8jXCp-XYml0EDexGHCBHRMt9QO64li3sTJKh4k2h7LAZkVb0Zb8BW6RTSHbzNVJSXEp-dLkCqpvbRrKtXQbX6ONS2t-I0Mva3GTfkdJm1Urd6fk2854W0ok7dIZ2WYtMcQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg01633.html . When I type the command, there was none:

echo $MINC_BIN_DIR

Any advise would be highly appreciated. Lots of thanks.

Regards, Krystal

Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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