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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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
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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
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has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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:
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.
Thanks in advance!
Taylor Ariko