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
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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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.
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" fischl@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" 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
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@nmr.mgh.harvard.edu
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Bruce Fischl -
John Anderson