Dear Bruce, In fact, when I run:
tkmedit subject2 brainmask.mgz lh.orig lh.white -aux wm.mgz -aux-surface rh.orig rh.white it gave me an error saying that tkmedit does not recognize lh.orig but the green line pops up and the orig surface button is now active. Why I still get the error message I don't know. I want to ask one more favour: 1).Can you please briefly describe the difference between the following files: orig.mgz brain.mgz brainmask.mgz T1.mgz 2) What is the difference between wm.mgz and filled.mgz 3) What represents the nu.mgz? Thank you. Antonella ________________________________ From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> To: Antonella Kis <ator...@yahoo.com> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, July 28, 2011 11:15 AM Subject: Re: "orig surface" button Hi Antonella, if it's not active then it probably failed loading the orig surface. Can you send us the output of the tkmedit command? There is a multi-view button you can click in tkmedit to show 3 orthogonal views at the same time. cheers Bruce On Thu, 28 Jul 2011, Antonella Kis wrote: > > Hi Bruce, > > Thanks again for your valuable information. I was trying to click on my "orig > surface" button in the interface but it is not active. Is there > a way that I can enable this option/button? I see more buttons are not > active. How I can fix this? > > Second, using tkmedit, how I can see the same point that I choose in one view > for example the coronal view in another view example horizontal > view? How I can select this point in one view and make it visible in another > view? > > Thanks, > Antonella > > ______________________________________________________________________________________________________________________________________________ > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > To: Antonella Kis <ator...@yahoo.com> > Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Sent: Wednesday, July 27, 2011 4:35 PM > Subject: Re: [Freesurfer] Corrections for the Pial surface > > Hi Antonella, > > 1. Can you load the lh.orig or rh.orig surface explicitly and see if it is > shown? Is the "orig surface" button clicked in the interface? > > 2. the hippocampus and amygdala are not neocortical structures and shouldn't > be included in the surfaces (in fact, the surfaces in those > regions are somewhat arbitrary as they don't have the laminar architecture we > are expecting). > > cheers > Bruce > > > On Wed, 27 Jul 2011, Antonella Kis wrote: > > > Hi Bruce, > > > > Thank again for your advice. I am not sure about the data collection but I > > will find out soon. In the mean time I have two more questions: > > 1). The FS tutorial shows for the surface outlines (by loading the -surfs) > > three line: the yellow indicating the white surface, the red for > > the pial and a green line for the orig data. When I plot the surfs I have > > only the yellow and red line. Can I get the green line somehow? > > 2). I suppose the two important brain structures, amygdala and hippocampus > > must be included in the pial surface as a grey matter (I hope I > am > > right) . > > If they are not enclosed in the pial surface is there a way to resolve > > this issue? How I should edit the pial surface in this case? How > > important is to have them enclosed for my cortical thickness studies and > > for the GLM group analysi? > > > > Thank you very much. > > Antonella > > > > > > > _______________________________________________ > 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. > > > >
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