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

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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:

http://secure-web.cisco.com/1y0hWbxxHjshrUwTJzNeSwAxHhObTdDFvMqX6XYU-SHaqbth...

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:d141bf4f-fbf2-44fa-b4f8-a90ce6065aea]

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

Best,

Krystal

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Krystal Xiwing Yau krystaly@hku.hk Sent: 15 May 2023 10:36:20 To: 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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: 12 May 2023 21:37:21 To: 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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