Hi Douglas,

Yes I can definitely do that!

After I run the recon -all part for a specific subject using freesurfer 7.2.0 in MATALB, I then run the below code:

%% 4c. Load Freesurfer Pre-Op MRI (do not edit)
addpath('/usr/local/freesurfer_x86_64-7.2.0/matlab');
fsmri_pre_acpc = ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);

Which gives me the following error:

/bin/bash: /scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh for reading
ERROR: loading /home/knight/ecog/DATA_FOLDER/UCSD/SD11/3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz as MGH
Dot indexing is not supported for variables of this type.

Error in ft_read_mri (line 401)
ndims = numel(size(tmp.vol));

Error in SD11_Recon_Pipeline (line 197)
fsmri_pre_acpc = ft_read_mri([subdir '3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);

I don't get this error when using freesurfer 6.0.0 and using those above commands. So I'm guessing it's because freesurfer 7.2.0 is trying to write something to a scratch file that doesn't even exist?

Thank you for your help!

Best,

Michael Ruvalcaba

Knight Lab

Helen Wills Neuroscience Institute

University of California, Berkeley

On Fri, Feb 23, 2024 at 10:26 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Can you send more info? Eg, command line, all terminal output, version of FS you are using?

On 2/6/2024 6:18 PM, Michael Ruvalcaba wrote:

External Email - Use Caution

Hello,

I had a similar question you had in the past thread (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/msg72609.html) but I cannot seem to access the link where you solved this issue. It looks like Tashrif helped you and he informed me to ask you

Can you help me with this by chance? I tried opening an account and logging in but it says my account hasn't been approved yet :( and I'm not sure who to contact to get it approved. It's been months.

Thank you!

Best,
Michael Ruvalcaba

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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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.