Those labels are for gray matter structures Cheers Bruce
> On Sep 7, 2015, at 6:48 PM, John Anderson <j.ander...@publicist.com> wrote: > > Hi Doug, > Thank you for your response. > When we open "wmparc.mgz" in freeview we can see clearly that we have labels > for cortical parcellations and it is white matter parcellations as well as > the unsegmented white matter > What is really confusing me is that deep structures like the thalamus, > amygdala, putamen, caudate, hypocampus .....etc are also labeled in > "wmparc.mgz". Are these labels means the white matter part of these segments > or it is gray and white matter together like the segments mentioed in > "aseg.mgz" ?! > > Please see the attached list of labels for one of my subjects. > > > 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 > > > Sent: Monday, September 07, 2015 at 1:02 PM > From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Segmenting deep and outer white matter > The best thing is to take a look at the wmparc. It was not really designed to > be deep and superficial. There is only one "deep" WM seg which is called > "Unsgemented White Matter" or something like that. > doug > > On 9/5/15 5:54 PM, Bruce Fischl wrote: > Hi John > > I defer to Doug. Not sure he ever published it though > Bruce > On Sat, 5 Sep 2015, John Anderson wrote: > > 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 > 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 > 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 > > > >_______________________________________________ > 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 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. > <Untitled.png> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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