Thank you Doug,

 

I was not able to test it as I was not able to create a symlink of Freesurfer outputs directly under subject folder (permission issues). We are running our data in a cluster and it follows a certain data structure and access rules.

 

Is there an alternate way to do so, how does mri_gtmpvc identify subject directory inherently?

 

Thank you,

Sneha

 

 

That is the way I would have suggested. Does it run to completion when you use the softlink? Reorganizing the folder structure it likely to break a lot of things.

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Dear team,

 

I am running mri_gtmpvc using RBV correction, however when I do so I get an error message saying it cannot find $SUBJECTS_DIR/$subject_id/mri/orig.mgz needed for RBV.

 

Our Freesurfer outputs are nested as $subject_id/MPRAGE/Freesurfer/mri/orig.mgz. I tried mri_gtmpvc with “--sd” flag as well, still same error as when I set “--sd $subject_id/MPRAGE/Freesurfer” it tries to find the file as $subject_id/MPRAGE/Freesurfer/$subject_id/mri/orig.mgz. One way I can avoid doing this is by creating a soft link with the expected path, however if there is a better way to do so that would be great.

 

Thank you,

Sneha

 

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