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" <fis...@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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