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

 

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
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

 

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