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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
To report a problem, see http://secure-web.cisco.com/1dFtz9tfZWpoyZVj7mXFMLhzADOYxytPQ-lAzdm9SS0VD1FT...
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. https://secure-web.cisco.com/1s_8L81vMyC0-KdGicsKrUniSkh4Egg5_LxXz-_YnmsgL0G... 2. https://secure-web.cisco.com/1MW6Y468pIeNLaB3ruN22mzrkJIjqalKQmsNncuNqyZW9S9...
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