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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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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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Douglas N. Greve -
Sneha Pandya