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
<dgr...@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
(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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