Hi Taylor,
I don't understand how you could get that error. It seems to me that
read_signa() is for reading .signa files.
Can you try 'mris_calc -o rh.area.mid rh.area add rh.area.pial' directly? Pass
full path to your rh.area and rh.area.pial.
What does 'mri_info rh.area' report?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read
access to rh.area
External Email - Use Caution
Hello FreeSurfer Developers,
I am attempting to run the recon-all pipeline on one subject using the
following code:
recon-all -all -i t1.nii -s p03_1
Although, I get the following error in the command line:
mris_calc -o rh.area.mid rh.area add rh.area.pial
error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 'rh.area'.
Tue Aug 1 15:58:13 EDT 2023
ERROR: vertexvol
mris_calc -o rh.area.mid rh.area add rh.area.pial
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
recon-all -s p03_8 exited with ERRORS at Tue Aug 1 15:58:13 EDT 2023
To report a problem, see MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://secure-web.cisco.com/1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FTbz45enl8IaOWz6IRp_KLvd-O07tGlRWlew0e-tEz_uiSd7h7vjXFLqsJ43sz_QtFlRODTxSyXDZGJH-L2KeK1nXuICROZ0fCFy4KhTJxJ3haAuYRWOZcUa5BBA0fS4iGoh92xzUyORn8wvcaGQ3GMrAFxd-bI-V_SZY3tfGjNWqrLPpayxctYehni827EcLH8K0REtJUxl1SPpG6Pe3Emtor75zz-0Hm9qjm0-uKKTYgh6I5B9-s-Y0K05FI459LrA6nQEDmQc7Af7uhtsjN1f1kK5Ejciw7kqOfhnQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>
The recon-all.error file contains:
------------------------------
SUBJECT p03_8
DATE Tue Aug 1 15:58:13 EDT 2023
USER taylorariko
HOST C02F10PVPN5W.local
PROCESSOR x86_64
OS Darwin
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b)
/Applications/freesurfer/7.2.0/bin/recon-all
PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri
CMD vertexvol --s p03_8 --rh --th3
I have made sure that I have read, write, and execute access to the folder
/path/to/subject/surf and the file rh.area. I can successfully run the command
to make rh.area (mris_place_surface --area-map ../surf/rh.white
../surf/rh.area), but the error persists in using rh.area. I have disk space
and can run other commands such as this fake one (mris_calc -o rh.area.Test
rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to
rerun the command from root and get the same error message.
I found 2 similar threads of the mail-archive, though I didn't find any
remedies:
1. MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44230.html<https://secure-web.cisco.com/1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0Gm5kE9GJdy_R08c77fGYQTPDdQWTXx7zHH94KsUkxY5QpVUmicO4epJQCmrRk9qMFABnrFnqeMNWHf8BMzYZT9-_q55fpDjwdwtbSup33zXWmZ7_Qaxd-4Z5VhTLIcQnzdH1PATkHpAO-TTMDS2pwJXoqBJWfCdjq5iu6ZD_6K0lrHqWnH3JudltTqMg3oGYhVXWbXscFSmN__-ZRnNfVJ8CDc90XN86oLWU105NH4AaObyV0lLfIM82_MyoJeAcNXkfuOpxqrOcWWH_mbDB5W0KbiD_DVkA4CTMYOqPQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44230.html>
2. MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51444.html<https://secure-web.cisco.com/1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S97Lqt_NIPp9ILpSPWI1wipv6Yr0BpbNmGPSoS-nDLaWTSHWRvXjPBhx6OWaUG3ykAth8rcrPy56gCpMo8EJHuhvxzkr3J5a8gg_8hfpQn3rWeGwxvT0rbc0ADxMrz98-mzO1bI4_zT80IcHOH6lIka2UdyAuC6gQplfb_eWpXafHuJDUR-JbSxIKSJcWIraGWK6JhoVQfgB3PNWSVgFkCVarUhylVDULGGQwPvt8XCNNPOC-bX_PoKwRMM7irjngRXBU0TPYBqY3QjiI4O9FrPJMQEQNW3NadmyXb4uhQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg51444.html>
Does anyone have any thoughts on how to trouble-shoot this? I have included my
recon-all.log in the case it is of any use.
1. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
2. Platform: macOS Sonoma 14.3.1
3. uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0:
Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64
4. recon-all.log: see attached
Thanks in advance!
Taylor Ariko
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
