Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data.
After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues: 1. How can I add the CSF, the skull and the scalp in my model? I know that with FS you can get just WM and GM. 2. How can I convert the RAS coordinates to MNI ones?
I have been trying to look at these topics on line and on the FreeSurfer website, but I haven’t find anything useful so far.
Many thanks in advance for your help!
Best Regards Chiara
---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
Hi Chiara
you can look at the mri_watershed help to see how to generate other tissue classes or boundary models, but typically you need some other image contrast(s) like T2/PD. What are you trying to accomplish?
As for your second question, you should be able to use mri_surf2surf with the talairach.xfm to convert the surfaces to MNI coords, or just map to fsaverage which I believe is already in MNI space.
cheers Bruce
On Wed, 20 Apr 2016, Chiara Bulgarelli wrote:
Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data.
After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues:
- How can I add the CSF, the skull and the scalp in my model? I know that
with FS you can get just WM and GM. 2. How can I convert the RAS coordinates to MNI ones?
I have been trying to look at these topics on line and on the FreeSurfer website, but I haven’t find anything useful so far.
Many thanks in advance for your help!
Best Regards Chiara
Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
Many thanks Dr. Fischl for your support.
My goal is to create a mesh completed of skull and scalp to be able to perform the Monte Carlo simulation on it. To do it, I need to start from a well segmented brain, so I decided to go for FreeSurfer.
I have read something about the mri_watershed, but I could’t find any specific information about how exactly use it (my apologise, but I am quite new among the FreeSurfer users). Why do I need the T2 image to use this function?
Many thanks in advance
Best
Chiara
---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
On 20 Apr 2016, at 14:30, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Chiara
you can look at the mri_watershed help to see how to generate other tissue classes or boundary models, but typically you need some other image contrast(s) like T2/PD. What are you trying to accomplish?
As for your second question, you should be able to use mri_surf2surf with the talairach.xfm to convert the surfaces to MNI coords, or just map to fsaverage which I believe is already in MNI space.
cheers Bruce
On Wed, 20 Apr 2016, Chiara Bulgarelli wrote:
Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data. After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues:
- How can I add the CSF, the skull and the scalp in my model? I know that
with FS you can get just WM and GM. 2. How can I convert the RAS coordinates to MNI ones? I have been trying to look at these topics on line and on the FreeSurfer website, but I haven’t find anything useful so far. Many thanks in advance for your help! Best Regards Chiara
Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
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.
Hi Chiara,
look at the -surf option and the -useSRAS option
We often use multi-echo FLASH/ PD images for generating these surfaces, because standard MPRAGE type sequences lack contrast for bone, see figure 17 here: http://www.nmr.mgh.harvard.edu/~fischl/reprints/Neuroimage_Segonne_watershed...
hth d
On Wed, Apr 20, 2016 at 10:44 AM, Chiara Bulgarelli cbulga01@mail.bbk.ac.uk wrote:
Many thanks Dr. Fischl for your support.
My goal is to create a mesh completed of skull and scalp to be able to perform the Monte Carlo simulation on it. To do it, I need to start from a well segmented brain, so I decided to go for FreeSurfer.
I have read something about the mri_watershed, but I could’t find any specific information about how exactly use it (my apologise, but I am quite new among the FreeSurfer users). Why do I need the T2 image to use this function?
Many thanks in advance
Best
Chiara
Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
On 20 Apr 2016, at 14:30, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Chiara
you can look at the mri_watershed help to see how to generate other tissue classes or boundary models, but typically you need some other image contrast(s) like T2/PD. What are you trying to accomplish?
As for your second question, you should be able to use mri_surf2surf with the talairach.xfm to convert the surfaces to MNI coords, or just map to fsaverage which I believe is already in MNI space.
cheers Bruce
On Wed, 20 Apr 2016, Chiara Bulgarelli wrote:
Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data. After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues:
- How can I add the CSF, the skull and the scalp in my model? I know that
with FS you can get just WM and GM. 2. How can I convert the RAS coordinates to MNI ones? I have been trying to look at these topics on line and on the FreeSurfer website, but I haven’t find anything useful so far. Many thanks in advance for your help! Best Regards Chiara
Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
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.
You can use mkheadsurf to create a surface of the outside of the head
On 04/20/2016 10:59 AM, dgw wrote:
Hi Chiara,
look at the -surf option and the -useSRAS option
We often use multi-echo FLASH/ PD images for generating these surfaces, because standard MPRAGE type sequences lack contrast for bone, see figure 17 here: http://www.nmr.mgh.harvard.edu/~fischl/reprints/Neuroimage_Segonne_watershed...
hth d
On Wed, Apr 20, 2016 at 10:44 AM, Chiara Bulgarelli cbulga01@mail.bbk.ac.uk wrote:
Many thanks Dr. Fischl for your support.
My goal is to create a mesh completed of skull and scalp to be able to perform the Monte Carlo simulation on it. To do it, I need to start from a well segmented brain, so I decided to go for FreeSurfer.
I have read something about the mri_watershed, but I could’t find any specific information about how exactly use it (my apologise, but I am quite new among the FreeSurfer users). Why do I need the T2 image to use this function?
Many thanks in advance
Best
Chiara
Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
On 20 Apr 2016, at 14:30, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Chiara
you can look at the mri_watershed help to see how to generate other tissue classes or boundary models, but typically you need some other image contrast(s) like T2/PD. What are you trying to accomplish?
As for your second question, you should be able to use mri_surf2surf with the talairach.xfm to convert the surfaces to MNI coords, or just map to fsaverage which I believe is already in MNI space.
cheers Bruce
On Wed, 20 Apr 2016, Chiara Bulgarelli wrote:
Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am trying to segment some structural images of infants data. After the classical segmentation done with the ‘-recon all’ function, I am stuck with two issues:
- How can I add the CSF, the skull and the scalp in my model? I know that
with FS you can get just WM and GM. 2. How can I convert the RAS coordinates to MNI ones? I have been trying to look at these topics on line and on the FreeSurfer website, but I haven’t find anything useful so far. Many thanks in advance for your help! Best Regards Chiara
Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
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
freesurfer@nmr.mgh.harvard.edu
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