Hi Bruce,
Thank you for your response!
Actually, after reviewing multiple papers ( segmentation in Freesurfer) I found that using "wmparc.mgz" as an input in the command "mri_binarize" will enable me to create two mask ( depending on the white matter parcellate mentioned in wmparc.mgz): The first mask is for deep white matter and the second mask is for the outer white matter.
I am facing one problem right now. I don't know how to divide the white matter parcellates mentioned in "wmparc.mgz" into deep and outer parcellates. Is there any reference that can help. The number of the parcellate is very big and for the purposes of publication I need a reference to divide them.
Any help is highly appreciated.
Bests,
John Anderson
Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
John Anderson
Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
Sent: Saturday, September 05, 2015 at 4:23 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmenting deep and outer white matter
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Segmenting deep and outer white matter
Hi John
sorry, meant to respond but spaced it. Have you checked out the
wmparc.mgz? It may have what you need.
cheers
Bruce
On Sat, 5 Sep 2015, John Anderson
wrote:
> Hi Freesurfers,
> I am interested in studying the difference between the outer and deep white
> matter volume in my study groups.
>
> I am thinking in the following procedures:
> 1. If there is any way in Freesurfer to do segmentation for the white matter
> (only in the depth of 3 cm) starting from the cortex. Then second
> segmentation for the deep white matter. Is this possible in Freesurfer?
> 2. Creating a mask ( using mri_binarize) for all the superficial white
> matter Freesurfer's labels and another mask for the deep white matter ( how
> can I find the Freesurfer deep white matter labels and the outer white
> matter labels ?)
> 3. If there is any atlas that can separate the outer and deep white matter
> then running recon-all depending on this new atlas.
>
> Thanks in advance for any suggestion.
> John
>
>
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
>_______________________________________________
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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sorry, meant to respond but spaced it. Have you checked out the
wmparc.mgz? It may have what you need.
cheers
Bruce
On Sat, 5 Sep 2015, John Anderson
wrote:
> Hi Freesurfers,
> I am interested in studying the difference between the outer and deep white
> matter volume in my study groups.
>
> I am thinking in the following procedures:
> 1. If there is any way in Freesurfer to do segmentation for the white matter
> (only in the depth of 3 cm) starting from the cortex. Then second
> segmentation for the deep white matter. Is this possible in Freesurfer?
> 2. Creating a mask ( using mri_binarize) for all the superficial white
> matter Freesurfer's labels and another mask for the deep white matter ( how
> can I find the Freesurfer deep white matter labels and the outer white
> matter labels ?)
> 3. If there is any atlas that can separate the outer and deep white matter
> then running recon-all depending on this new atlas.
>
> Thanks in advance for any suggestion.
> John
>
>
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
>_______________________________________________
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.
