You can use use mri_binarize with --min 0.5 and it will take all labels
with value 1 and greater. You can create a bounding box with mri_mask
with the -bb option
On 5/4/2021 11:53 AM, Arman Avesta wrote:
External Email - Use Caution
Hi gang,
I have downloaded head MRIs of 1000 subjects from ADNI, together with
their FreeSurfer generated aparc+aseg.mgz files. I'm using them in a
3D deep learning network. These MRIs are 256 x 256 x 256, which is too
large for GPU training. Therefore, I'm trying to pre-process the
volumes by putting a bounding box around the brain, crop the image,
and then resize it to a smaller size (e.g. 64 * 100 * 100).
To put the bounding box around the brain, I need the brain mask. I
don't have access to the brainmasks of these subjects, so I'm trying
to use mri_extract_label to make brainmasks for them.
Is there a way to tell mri_extract_label to put together all labels in
one volume?
Best regards,
Arman
------------------------------------------------------------------------
*Arman Avesta, MD*
Radiology Resident & PhD Student
Yale School of Medicine & Yale Graduate School of Arts and Sciences
Email: arman.ave...@yale.edu
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