Hi Bruce, the mask is already binariz (min=0 ; max=1)
I tried
mri_mask T1.nii mask.nii output.nii
The output is a maked image meaning the structure behind the mask
I tried mri_binarize mask.nii --min 0 --max 1 output mask.nii then
mri_mask T1.nii output_mask.nii output.nii
And I still get the same output. What in behind the mask and what I want is T1 free of what in the mask. I am not sure what I am doing wrong. My appologies for asking to many times.
Sent: Thursday, June 15, 2017 at 1:32 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] substract images
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] substract images
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
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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>
>
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is
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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
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
