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Dear Yujing
Thanks a lot !!! It is my fault. When I build this freesurfer, there are some files do not correctly located in the install directory. Then I just copy them from a x86 cluster. However, because I'm using the latest version from git, there are some difference between this two version. The warnings you mentioned are the small bugs of the system, please ignore. Here's the context of /vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt. I think it is wrong.
login3$ cat /vol0004/hp200139/data/u12257/freesurfer/average/colortable_vpnl.txt # This is an LUT for the Juelich ytoarchitectonic atlas surface labels created by Dr. Kalanit # Grill-Spector's Lab at the Stanford Vision and Perception Neuroscience Lab # See http://secure-web.cisco.com/1x8F5IrihAeNnPlynD7_olcHXVSCyGjMFfs6xdqCDrtm6LdZ... # Ref: Rosenke, M., Weiner, K. S., Barnett, M., Zilles, K., Goebel, # R., Grill-Spector, K. (2017). A cross-validated cytoarchitectonic # atlas of the human ventral visual stream. NeuroImage, # http://secure-web.cisco.com/1p99Xaij8ZyvGzIoi_dK2BOanzxbIArwmyfHduwxdPLnMCKX... 1 FG1 57 255 20 0 2 FG2 255 0 255 0 3 FG3 0 0 255 0 4 FG4 109 7 26 0 5 hOc1 0 100 0 0 6 hOc2 255 0 0 0 7 hOc3v 0 255 255 0 8 hOc4v 255 255 0 0
In https://secure-web.cisco.com/1rL_wmTmlepQKLEY0nBYoGUCBDcZbJgmQoAKwfu58LxxgoQ..., it should be:
# This is an LUT for the Juelich ytoarchitectonic atlas surface labels created by Dr. Kalanit # Grill-Spector's Lab at the Stanford Vision and Perception Neuroscience Lab # See http://secure-web.cisco.com/1x8F5IrihAeNnPlynD7_olcHXVSCyGjMFfs6xdqCDrtm6LdZ... # Ref: Rosenke, M., Weiner, K. S., Barnett, M., Zilles, K., Goebel, # R., Grill-Spector, K. (2017). A cross-validated cytoarchitectonic # atlas of the human ventral visual stream. NeuroImage, # http://secure-web.cisco.com/1p99Xaij8ZyvGzIoi_dK2BOanzxbIArwmyfHduwxdPLnMCKX... 1 FG1.mpm.vpnl 57 255 20 0 2 FG2.mpm.vpnl 255 0 255 0 3 FG3.mpm.vpnl 0 0 255 0 4 FG4.mpm.vpnl 109 7 26 0 5 hOc1.mpm.vpnl 0 100 0 0 6 hOc2.mpm.vpnl 255 0 0 0 7 hOc3v.mpm.vpnl 0 255 255 0 8 hOc4v.mpm.vpnl 255 255 0 0
Sincerely,
Tianxiang Lyu Graduate School of Medicine, Juntendo University
Huang, Yujing YHUANG43@mgh.harvard.edu 于2024年5月7日周二 21:57写道：
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-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.
- download these two colortables from Freesurfer repo - *MailScanner has
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distribution/average/colortable_BA_thresh.txt
distribution/average/colortable_vpnl.txt
- 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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