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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://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

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...

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
External Email - Use Caution
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 forum . When I type the command, there was none:

echo $MINC_BIN_DIR

Any advise would be highly appreciated. Lots of thanks.

Regards,
Krystal

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