Fantastic!!
It is worked. Thank you very much for the great help!
Sent: Thursday, June 15, 2017 at 1:51 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
try:
mri_binarize mask.nii --min 0 --max .1 --o mask.rev.nii --binval 1
mri_mask T1.nii mask.rev.nii T1.masked.nii
cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:
> 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
> 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
> > 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.
>
>_______________________________________________
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.
mri_binarize mask.nii --min 0 --max .1 --o mask.rev.nii --binval 1
mri_mask T1.nii mask.rev.nii T1.masked.nii
cheers
Bruce
On Thu, 15 Jun 2017, John Anderson wrote:
> 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
> 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
> > 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
> 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.
