It can't find the file struct.nii. You have to give it the full path to the file. It looks like $Users is not set to anything (blank)

On 6/28/2024 12:03 AM, Lydia Luck wrote:

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Hello-

I am trying to do recon-all on my brain MRI and I’ve rewritten it so many times I have absolutely no clue what is going wrong. Ultimately, the main error message I’m getting is that my file is not found. I’ve tried typing out the complete path, made multiple different folders, renamed the file and the folders, changed the file type, changed the location of the folder, exited terminal and tried again, switched to the other user on the computer (got the same error) even restarted my computer, etc. Kind of at a loss at this point. I am using a Mac with an M1 chip and the 7.4.1 version

This is my current line of commands:

export FREESURFER_HOME=/Applications/freesurfer/7.4.1

source $FREESURFER_HOME/SetUpFreeSurfer.sh

export FS_LICENSE=/opt/freesurfer/license.txt

export SUBJECTS_DIR=$Users/lydialuck/3DBRAIN

recon-all -s lydiasbrain -i $Users/lydialuck/3DBRAIN/struct.nii.gz -parallel -all

And then getting this back:

ERROR: cannot find /lydialuck/3DBRAIN/struct.nii.gz

Darwin Blazes-MBP.lan 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:06 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T8103 arm64

recon-all -s lydiasbrain exited with ERRORS at Thu Jun 27 01:13:56 EDT 2024

If you could help me figure this out that would be great; I’ve probably spent well over 6 hours now trying different things.

Thanks so much,

Lydia
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