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Hello FreeSurfer Developers,
I found what I believe to be a bug. Typically I can load mgz files into my
Matlab program without any trouble.
But if the path containing the mgz file has a space then I get an error.
When I run this very short script in Matlab calling the MRIread function
(/Applications/freesurfer/7.4.1/matlab/MRIread.m):
filepath = char("/Users/user/Documents/folder space test/data/mri.mgz");
mri = MRIread(filepath);
I get the following error:
gunzip: can't stat: /Users/user/Documents/folder
(/Users/user/Documents/folder.gz): No such file or directory
gunzip: can't stat: space (space.gz): No such file or directory
gunzip: can't stat: test/data/mri.mgz (test/data/mri.mgz.gz): No such file or
directory
ERROR: problem reading fname
SWITCH expression must be a scalar or a character vector.
Error in load_mgh (line 163)
switch type
Error in MRIread (line 90)
[mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
Error in test_load_mgz (line 2)
mri = MRIread(filepath);
I traced this down to the function load_mgh.m
(/Applications/freesurfer/7.4.1/matlab/load_mgh.m) where a file path string
(char array) is dynamically populated with randomly generated folder names to
unzip into.
It's about line 69 and looks like this:
[status,msg] = unix(sprintf('gunzip -c %s > %s', fname, new_fname));
You may notice that potential spaces in the path names fname and new_fname are
not escaped with single quotes.
I edited the file to escape the parameterized strings like so:
[status,msg] = unix(sprintf("gunzip -c '%s' > '%s'", fname, new_fname));
This solved the problem for me.
Computer details:
OS: MacOS Sonoma (latest)
Chipset: Apple M1 (aarch64)
Calling Program: Matlab R2023b
Freesurfer: 7.4.1
Thank you for your time.
Sincerely,
Tyler Slouf_______________________________________________
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