That is weird -- ft_read_mri is not one of our files. Can you send the command line and the *full* terminal output? The lGI stuff is pretty old and does not have a maintainer.

On 2/26/2024 1:40 PM, Michael Ruvalcaba wrote:

External Email - Use Caution

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:

...

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Hello,

I had a similar question you had in the past thread
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg72609.html
<https://secure-web.cisco.com/1zJkMv9aRmMM6PokM8jDCRUGLybtdGCgeH3ZTgzjLrgSV_Psg_PyipqWV0v3sXbvB4_kb2A09lkKzETq6p-Q72y_fLJpYAnivZ4sE6U8wa3OLcRcFsJk0pDqWI3jzvqCxrbp0pnCYTzlhRCne1CYNAdMoxB0ORfhE16LGiGIx3c7zpeRHDvzb_WkvNj-0ed0Xhwjs6Moiijl9lhtwkJHIFunH6CWkBHCO9YRg23zb5D0wWbxRcR5VBiMAEUQbw6m5cecc6wHXPMoaR8R0dYuln5D7FyLEF2jkY7VCKhKPrZBwR4aZ2PiSMztXbtH6So-p/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg72609.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

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