Can you check if the colortables from your install directory agree with git
repo?
/vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt
/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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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-uch...@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 <yhuan...@mgh.harvard.edu<mailto:yhuan...@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<https://secure-web.cisco.com/1yaJ9rtkF1pEnV3tBbwmzU19ZQQLWvibkvCE5WtM29vK2Qhee6eSfVg9hY75lhno1A0Q0zlRCN9D2we_SqyfSnlM8y0afWtm4g13yqgPYioYdjztyvi6knI0BIwx4sBnX2SY6hXES8QI1F7WNZ8NKk-H6HVwQ4LhI_6wKFlEL023LFxXzlhNLpMPl2TbPyHG_8PIMXBsXRSzfs-4t9DvHm1Z1OX8gSbHtqSvyCTbTo-_KDEaLFQmpTk6buYNbfAxhMv5_0keYI6iPJ7KZIHHjXWdgKEB_7BhnysWX6TbYYwPmizpsRsVGwlF40Ulqm46c/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer.git>
distribution/average/colortable_BA_thresh.txt
distribution/average/colortable_vpnl.txt
2. copy them to your average/ directory
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of LYU, TIANXIANG
Sent: Tuesday, May 7, 2024 12:30 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: 内田航 <w-uch...@juntendo.ac.jp<mailto:w-uch...@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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