External Email - Use Caution        

Hello Yujing,

 

 

Thank you for your quick response!

 

 

When I run:

 

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add /path/to/subject/surf/rh.area.pial

 

I get the following error:

 

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 '/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.

 

 

But when I run:

 

mri_info rh.area

 

I get the following output:

 

Volume information for rh.area

          type: unknown

    dimensions: 831 x 10015 x 25953

   voxel sizes: -0.000000, -0.000000,    nan

          type: SHORT (4)

           fov: 1016.473

           dof: 1

        xstart: 0.0, xend: 990983162970892849632569550308376576.0

        ystart: -0.0, yend: 3079152361728581627851833344.0

        zstart: -0.0, zend: -3815443229699337177012458129513775104.0

            TR: 0.00 msec, TE: -0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees

       nframes: 1

       PhEncDir: UNKNOWN

       FieldStrength: 0.000000

ras xform present

    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r = -18770011487391973376.0000

              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =        nan

              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =    -0.0000

Orientation   : LIA

Primary Slice Direction: coronal

 

voxel to ras transform:

                0.0000  -0.0000      nan        nan

               -0.0000  -0.0000      nan        nan

               -0.0000   0.0000      nan        nan

                0.0000   0.0000   0.0000     1.0000

 

voxel-to-ras determinant nan

 

ras to voxel transform:

error: mat = NULL!

 

 

It appears that this is where the issue is coming from. Any ideas on why this is occurring? The brain is normal and has good rh.white and rh.pial surfaces.

 

 

Many thanks,

Taylor

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Date: Tuesday, March 5, 2024 at 4:25 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area

CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.

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

 

        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

 

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