Hi Jon
use mri_binarize on your initial mask to create a new one for mri_mask (use --min and --max to specify the input mask intensity ranges that you want to be "on"), then give that to mri_mask
cheers Bruce On Thu, 15 Jun 2017, John Anderson wrote:
Thank you Dr Bruce
mri_mask removes everything and leaves the areas behind the mask. And what I want is the opposite. For example with mri_mask if I have brain with skull and mask for skull stripped brain then the output is skull stripped brain. What I want is the opposite, the skull without the brain. I highly aprreciate any suggestion. Sent: Thursday, June 15, 2017 at 1:19 PM From: "Bruce Fischl" fischl@nmr.mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] substract images Hi Jon
mri_mask should do the trick
cheers Bruce On Thu, 15 Jun 2017, John Anderson wrote:
Dear experts, I have image and mask and I want to subtract the mask from the image. Meaning I want to get image free of specific anatomical region. For
example,
I have image T1.nii for the brain and mask for the thalamus. How can I remove the thalamus from the T1 image to get T1 image free of the
thalamus.
Thanks you for any help Jon
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