External Email - Use Caution
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
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Friday, July 12, 2024 9:22 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] mri_gtmpvc RBV - cannot find file from a
custom subject directory
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. On 7/11/2024 10: 02 AM, Sneha Pandya wrote: External Email - Use
Caution Dear
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.
On 7/11/2024 10:02 AM, Sneha Pandya wrote:
External Email - Use Caution
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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