[Freesurfer] Numerical values of cortical thickness in average subject

Hi, I'm new to freesurfer and I'd like to know how I can have access to the numerical values of the cortical thickness of an average subject. Thanks. Inês ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mai

[Freesurfer] Create thickness map

Hello, Is it possible to create a "fake" thickness map in order to perform some tests? Thanks, Ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Fake thickness map 2

Hello, I was trying to create a cortical thickness map with constant values in order to perform some tests. At first I tried using mris_convert. I converted my thickness file into ascii: mris_convert lh.thickness lh.thickess.asc then I used matlab to change all the values in the last column to 2

[Freesurfer] Fake thickness map 2

-- Forwarded message -- From: Bruce Fischl <[EMAIL PROTECTED]> Date: 06/08/2007 14:23 Subject: Re: [Freesurfer] Fake thickness map 2 To: Inês Souta <[EMAIL PROTECTED]> they don't matter. For a real volume they would be the ras2vox transform and the mr parameters.

Re: [Freesurfer] Fake thickness map 2

freesurfer v.3.0.5 for Linux-Centos4 2007/8/6, Bruce Fischl <[EMAIL PROTECTED]>: > > yes, you should be able to open it in tksurfer. What version of > freesurfer do you have? > On Mon, 6 Aug 2007, Inês Souta wrote: > > > And after creating the mgh volume, how can I

Re: [Freesurfer] Fake thickness map 2

Sorry, I was saving it with the wrong extension. I am already able to open it in tksurfer! Thanks a lot, Ines 2007/8/6, Inês Souta <[EMAIL PROTECTED]>: > > freesurfer v.3.0.5 for Linux-Centos4 > > > 2007/8/6, Bruce Fischl <[EMAIL PROTECTED]>: > > > >

Re: [Freesurfer] Fake thickness map 2

purposes they can be any 4x4 and you can > leave the mri_parms one out (it will detect and fill it in with zeros). > > Send these to the list so other people can answer! > > Bruce > On > Mon, 6 Aug 2007, Inês Souta wrote: > > > Hi again, > > > > I still don&#x

[Freesurfer] Excluded gray matter - pial surface

Hi there, I need to edit the pial surface. It isn't getting out far enough all over the cortex. I'm sure it is not a skull stripping problem. Do I need to add control points everywhere in order to correct this? Isn't there another way? Thanks Ines ___

[Freesurfer] Standard deviation map

Hello, After computing the average thickness of an average subject (prior to Qdec), how can I estimate and get a map of standard deviations of the thickness measures across the subjects I've averaged. Thanks, Ines ___ Freesurfer mailing list Freesurfer

[Freesurfer] Switch hemispheres

Hi, After processing the hole image I realized that the orientation of the original .mgz file was wrong and I've ended up with switched hemispheres. The right hemisphere is where the left should be, and vice-versa. Otherwise the orientation is right. Since I've already made manual edits, is the an

Re: [Freesurfer] Switch hemispheres

AIL PROTECTED]>: > > I think you can: > > rename the lh.* files to xx.* > > rename the rh.* files to lh.* > > rename the xx.* files to rh.* > > > > > > *From:* [EMAIL PROTECTED] [mailto: > [EMAIL PROTECTED] *On Behalf Of *Inês Souta > *Sent:* quinta

[Freesurfer] Convert values in label

Hi again, Is there any way to have access to the numerical values of cortical thickness in an ROI? Thanks, Ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Convert values in label

Yes, it will! thanks a lot Inês 2007/9/8, Bruce Fischl <[EMAIL PROTECTED]>: > > I think if you load the label and load the thickness as an overlay, then > save the label it will put the thickness values into the last column of > the label file. > > cheers, > Bruce

Re: [Freesurfer] Switch hemispheres

autorecon3 I think would do it) > > On Thu, 6 Sep 2007, Pedro Paulo Oliveira Jr wrote: > > > I think you can: > > > > rename the lh.* files to xx.* > > > > rename the rh.* files to lh.* > > > > rename the xx.* files to rh.* > > > > > &

[Freesurfer] Standard deviation map

Hi there, How can I get a standard deviation map of the thickness measurements ina subject? Inês ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Standard deviation map

but that doesn't sound like what you mean. > > Bruce > > > On Thu, 20 Sep 2007, Inês Souta wrote: > > > Hi there, > > > > How can I get a standard deviation map of the thickness measurements ina > > subject? > > > > Inês > > ___

Re: [Freesurfer] Standard deviation map

that interesting because the > thickness varies with geometry (e.g. sulci are thinner than gyri). > > cheers, > Bruce > > > On Thu, 20 Sep 2007, Inês Souta wrote: > > > Well, I'm dealing with a patient with an heterogeneous lesion. Somehow, > the > > lesion area see