Hello, I have run recon-all for my subject, if I want to get more subcortical segmentation, e.g., globus pallidus, medulla, pons and so on, how can I do?Can I manually draw these region on the bert image and transfer them to individual subject, like mri_label2label? Thanks. Lisa
Hi Lisa
globus pallidus is included in the aseg, have you looked at it? The others you could lab on the fsaverage volume and warp to individual subjects if you want, but that won't be as accurate as including them in our atlas (but a lot easier!). We are working on segmenting things like medulla and pons, but it's not ready for prime-time yet.
cheers Bruce
On Thu, 5 Sep 2013, Luo,Yishan wrote:
Hello, I have run recon-all for my subject, if I want to get more subcortical segmentation, e.g., globus pallidus, medulla, pons and so on, how can I do? Can I manually draw these region on the bert image and transfer them to individual subject, like mri_label2label?
Thanks.
Lisa
Dear Bruce,
Is globus pallidus in aseg named pallidum, as I only see this? For labeling the regions, should I do the following steps, please correct if I am wrong. 1. use tkmedit to draw the region on fsaverage question: should these regions be drawn as segmentation or label? 2. then use mri_label2label to transfer the label to individual subject question: if step1 uses segmentation, how can I transfer it to label? and in the label2label function, for the --regmethod option, should I use volume? Thanks a lot for your answering. Best Regards,Lisa
Date: Thu, 5 Sep 2013 09:03:36 -0400 From: fischl@nmr.mgh.harvard.edu To: lys84818@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] new subcortical regions
Hi Lisa
globus pallidus is included in the aseg, have you looked at it? The others you could lab on the fsaverage volume and warp to individual subjects if you want, but that won't be as accurate as including them in our atlas (but a lot easier!). We are working on segmenting things like medulla and pons, but it's not ready for prime-time yet.
cheers Bruce
On Thu, 5 Sep 2013, Luo,Yishan wrote:
Hello, I have run recon-all for my subject, if I want to get more subcortical segmentation, e.g., globus pallidus, medulla, pons and so on, how can I do? Can I manually draw these region on the bert image and transfer them to individual subject, like mri_label2label?
Thanks.
Lisa
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Hi Lisa
you can use mri_vol2vol if you are generating segmentation volumes that you want warped, and you will want to use the talairach.m3z for volume warping
cheers Bruce
On Fri, 6 Sep 2013, Luo,Yishan wrote:
Dear Bruce,
Is globus pallidus in aseg named pallidum, as I only see this?
For labeling the regions, should I do the following steps, please correct if I am wrong.
- use tkmedit to draw the region on fsaverage
question: should these regions be drawn as segmentation or label?
- then use mri_label2label to transfer the label to individual subject
question: if step1 uses segmentation, how can I transfer it to label? and in the label2label function, for the --regmethod option, should I use volume?
Thanks a lot for your answering.
Best Regards, Lisa
Date: Thu, 5 Sep 2013 09:03:36 -0400 From: fischl@nmr.mgh.harvard.edu To: lys84818@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] new subcortical regions
Hi Lisa
globus pallidus is included in the aseg, have you looked at it? The others you could lab on the fsaverage volume and warp to individual subjects if you want, but that won't be as accurate as including them in our atlas (but a lot easier!). We are working on segmenting things like medulla and pons, but it's not ready for prime-time yet.
cheers Bruce
On Thu, 5 Sep 2013, Luo,Yishan wrote:
Hello, I have run recon-all for my subject, if I want to get more subcortical segmentation, e.g., globus pallidus, medulla, pons and so on, how can I do? Can I manually draw these region on the bert image and transfer them to individual subject, like mri_label2label?
Thanks.
Lisa
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
-
Bruce Fischl -
Luo,Yishan