Can you check if the colortables from your install directory agree with git repo?

/vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt

In your recon-all.log, there are a lot of warning messages like the following. I don’t know what that means.

“

[WARN] xos LPG 2002 - Failed to map HugeTLBfs for data/bss: /usr/bin/sed

The e_type of elf header must be ET_EXEC when using libmpg. You can check it on your load module by readelf -h command.

[WARN] xos LPG 2002 - Failed to map HugeTLBfs for data/bss: /usr/bin/uptime

The e_type of elf header must be ET_EXEC when using libmpg. You can check it on your load module by readelf -h command.

[WARN] xos LPG 2003 - Failed to map HugeTLBfs for data/bss: Layout problem with segments 0 and 1:

Segments would overlap.

“

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of LYU, TIANXIANG
Sent: Tuesday, May 7, 2024 8:36 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: 内田航 <w-uchida@juntendo.ac.jp>
Subject: Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

External Email - Use Caution

Dear Yujing,

I hope this email finds you well.

I've checked the directory. /average/colortable_vpnl.txt and ./average/colortable_BA_thresh.txt are both as the same as the ones in the git repo.

Also, the label files have been successfully generated in the subject’s label directory.

I build this freesurfer on our own aarch64 cpu, with the current source code of git repo. Should I try the source code of 7.4.1? which works well with its x64 binaries on my intel-based cluster, but I'm not sure whether the problem can be solved on this aarch64 cpu.

Sincerely,

Tianxiang Lyu

Graduate School of Medicine,

Juntendo University

Huang, Yujing <YHUANG43@mgh.harvard.edu> 于2024年5月7日周二 21:23写道：

Your recon-all should have generated the following label files in your subject’s label directory:

label/?h.FG1.mpm.vpnl.label

label/?h.FG2.mpm.vpnl.label

label/?h.FG3.mpm.vpnl.label

label/?h.FG4.mpm.vpnl.label

label/?h.hOc1.mpm.vpnl.label

label/?h.hOc2.mpm.vpnl.label

label/?h.hOc3v.mpm.vpnl.label

label/?h.hOc4v.mpm.vpnl.label

I don’t know how you got your Freesurfer distributions. But it looks like your average/colortable_vpnl.txt is out of sync with mris_label2annot.

1. download these two colortables from Freesurfer repo - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/freesurfer/freesurfer.git

distribution/average/colortable_BA_thresh.txt

distribution/average/colortable_vpnl.txt

2. copy them to your average/ directory

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of LYU, TIANXIANG
Sent: Tuesday, May 7, 2024 12:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: 内田航 <w-uchida@juntendo.ac.jp>
Subject: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to process recon-all commands, but in mris_label2annot command:

ERROR: FG1.mpm.vpnl not found in CTAB /vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt
Command exited with non-zero status 1
@#@FSTIME 2024:05:07:07:05:22 mris_label2annot N 26 e 4.35 S 0.34 U 2.65 P 68% M 203264 F 4 R 3608 W 0 c 0 w 1728 I 18304 O 0 L 0.92 0.91 0.96

I've checked the directory, but find nothing strange. (file colortable_vpnl.txt exists)

I've searched the list and no similar errors have been reported. 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.

Sincerely,

Tianxiang Lyu

Graduate School of Medicine,

Juntendo University

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