External Email - Use Caution
Hi Freesurfer email list,
I'm trying to get the midbrain mask from the brainstem segmentation pipeline into standard space, for use in analyzing some data in other modalities. I have labeled T1s in individual-space (it's a longitudinal pipeline). Does the brainstem atlas already exist somewhere in MNI-space as a mask? If so, where could I find it? I've found the ROI mesh data, but I don't know how to convert that into a voxel mask.
Thanks so much, -Dan Peterson
Hi Dan
which brainstem atlas do you mean?
cheers Bruce
On Wed, 30 May 2018, djpeters@u.washington.edu wrote:
External Email - Use CautionHi Freesurfer email list,
I'm trying to get the midbrain mask from the brainstem segmentation pipeline into standard space, for use in analyzing some data in other modalities. I have labeled T1s in individual-space (it's a longitudinal pipeline). Does the brainstem atlas already exist somewhere in MNI-space as a mask? If so, where could I find it? I've found the ROI mesh data, but I don't know how to convert that into a voxel mask.
Thanks so much, -Dan Peterson
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
The "brainstem pipeline" described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
Thanks! -Dan
On Wed, 30 May 2018, Bruce Fischl wrote:
Hi Dan
which brainstem atlas do you mean?
cheers Bruce
On Wed, 30 May 2018, djpeters@u.washington.edu wrote:
External Email - Use CautionHi Freesurfer email list,
I'm trying to get the midbrain mask from the brainstem segmentation pipeline into standard space, for use in analyzing some data in other modalities. I have labeled T1s in individual-space (it's a longitudinal pipeline). Does the brainstem atlas already exist somewhere in MNI-space as a mask? If so, where could I find it? I've found the ROI mesh data, but I don't know how to convert that into a voxel mask.
Thanks so much, -Dan Peterson
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
External Email - Use Caution
Hi Dan,
The mesh can be rasterized in its reference space, but such does not correspond to any volumetric image.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of djpeters@u.washington.edu djpeters@u.washington.edu Sent: Wednesday, May 30, 2018 10:51:38 PM To: Freesurfer support list Subject: Re: [Freesurfer] midbrain mask in standard-space?
External Email - Use Caution
The "brainstem pipeline" described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
Thanks! -Dan
On Wed, 30 May 2018, Bruce Fischl wrote:
Hi Dan
which brainstem atlas do you mean?
cheers Bruce
On Wed, 30 May 2018, djpeters@u.washington.edu wrote:
External Email - Use CautionHi Freesurfer email list,
I'm trying to get the midbrain mask from the brainstem segmentation pipeline into standard space, for use in analyzing some data in other modalities. I have labeled T1s in individual-space (it's a longitudinal pipeline). Does the brainstem atlas already exist somewhere in MNI-space as a mask? If so, where could I find it? I've found the ROI mesh data, but I don't know how to convert that into a voxel mask.
Thanks so much, -Dan Peterson
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
External Email - Use Caution
Thanks for responding, is there some known mapping of this reference space to MNI-space or another standard space?
On Wed, 30 May 2018, Iglesias Gonzalez, Eugenio wrote:
External Email - Use Caution
Hi Dan,
The mesh can be rasterized in its reference space, but such does not correspond to any volumetric image.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of djpeters@u.washington.edu djpeters@u.washington.edu Sent: Wednesday, May 30, 2018 10:51:38 PM To: Freesurfer support list Subject: Re: [Freesurfer] midbrain mask in standard-space? External Email - Use Caution
The "brainstem pipeline" described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
Thanks! -Dan
On Wed, 30 May 2018, Bruce Fischl wrote:
Hi Dan
which brainstem atlas do you mean?
cheers Bruce
On Wed, 30 May 2018, djpeters@u.washington.edu wrote:
External Email - Use Caution
Hi Freesurfer email list,
I'm trying to get the midbrain mask from the brainstem segmentation pipeline into standard space, for use in analyzing some data in other modalities. I have labeled T1s in individual-space (it's a longitudinal pipeline). Does the brainstem atlas already exist somewhere in MNI-space as a mask? If so, where could I find it? I've found the ROI mesh data, but I don't know how to convert that into a voxel mask.
Thanks so much, -Dan Peterson
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Hi Dan
do you have he voxel segmentations of your data in subject space? If so, you can use mri_vol2vol and the subject's transforms/talairach.lta to map it into MNI space
cheers Bruce On Wed, 30 May 2018, djpeters@u.washington.edu wrote:
External Email - Use CautionThanks for responding, is there some known mapping of this reference space to MNI-space or another standard space?
On Wed, 30 May 2018, Iglesias Gonzalez, Eugenio wrote:
External Email - Use Caution
Hi Dan,
The mesh can be rasterized in its reference space, but such does not correspond to any volumetric image.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College London
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of djpeters@u.washington.edu djpeters@u.washington.edu Sent: Wednesday, May 30, 2018 10:51:38 PM To: Freesurfer support list Subject: Re: [Freesurfer] midbrain mask in standard-space? External Email - Use Caution
The "brainstem pipeline" described here:
https: //surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
Thanks! -Dan
On Wed, 30 May 2018, Bruce Fischl wrote:
Hi Dan
which brainstem atlas do you mean?
cheers Bruce
On Wed, 30 May 2018, djpeters@u.washington.edu wrote:
External Email - Use Caution
Hi Freesurfer email list,
I'm trying to get the midbrain mask from the brainstem segmentation pipeline into standard space, for use in analyzing some data in other modalities. I have labeled T1s in individual-space (it's a longitudinal pipeline). Does the brainstem atlas already exist somewhere in MNI-space as a mask? If so, where could I find it? I've found the ROI mesh data, but I don't know how to convert that into a voxel mask.
Thanks so much, -Dan Peterson
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https: //mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
djpeters＠u.washington.edu -
Iglesias Gonzalez, Eugenio