Re: [Freesurfer] --paired-diff option

Hi If you have pairs of one group then you need to specify one class.lets say subj1 and subj2 belong to one pair and subj3 and subj4 are also one pair. class maininput subj1 maininput subj2 maininput subj3 maininput subj4 main If you have two groups then you would need to specify two groups.class

[Freesurfer] surface

Hi, here's an email from Don Hagler from February 2009: It seems to me that vertex areas in the native subject space are not > meaningful. The orig surfaces should be uniformly tesselated; however, > topology correction and final surface finding should introduce complicated > and probably unint

Re: [Freesurfer] how to convert our own atlas to freesurfer

oh, then you would just replace the .gca file in mri_em_register, mri_ca_register, mri_ca_label and mri_ca_normalize cheers Bruce On Thu, 3 Dec 2009, Guang Zeng wrote: > > Hello, Bruce, > > It is a subcortical structure atlas based on 100 subjects. > > > Thanks a lot! > Guang > >> Date: Wed, 2

Re: [Freesurfer] surface

I think they are not interesting on a vertex-by-vertex basis, but over regions they are. cheers Bruce On Thu, 3 Dec 2009, j janssen wrote: > Hi, > > here's an email from Don Hagler from February 2009: > > It seems to me that vertex areas in the native subject space are not >> meaningful. The or

Re: [Freesurfer] how to convert our own atlas to freesurfer

Hello, Bruce, Thanks a lot! But which commands I can use to convert our atlas to the .gca format? Guang > Date: Thu, 3 Dec 2009 07:25:29 -0500 > From: fis...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] how to convert our o

Re: [Freesurfer] how to convert our own atlas to freesurfer

mri_ca_train compiles the statistics across subjects and creates a .gca. Search our wiki and you should find a page on how to do it On Thu, 3 Dec 2009, Guang Zeng wrote: > > Hello, Bruce, > > Thanks a lot! > But which commands I can use to convert our atlas to the .gca format? > > Guang > >> Da

[Freesurfer] check talairach transform

Hi, I run recon-all -autorecon1 on my own data set. I want to check the talairach transformation using tkregister2, but I don't have the "surf orig" (green lines) yet. My questions are: 1- How can I aligned the TARGET and MOVEABLE without the green lines? 2- Which of the 30 steps of recon-all -all

Re: [Freesurfer] check talairach transform

Hi Anne, 3 is best I think. Things rarely fail these days so you are better off just running them through and checking at the end. The orig surf is actually created twice - once by mri_tessellate then again by mris_fix_topology. cheers Bruce On Thu, 3 Dec 2009, Anne Gallagher wrote: > Hi, >

[Freesurfer] roisummary question

Hello Everyone, I'm unable to replicate my visual data with %signal change values in a between group analysis. If anyone has time to look at this and offer help, I'd be very appreciative. Here are the steps I'm taking: 1. I'm running an event-related analysis with 5 conditions. I'm interested

[Freesurfer] Neonatal Brain

Followup to yesterdays question - there is one Freesurfer paper I know of that did segmentation (and curvature analysis) of newborn brains. Bruce, you are a co-author, could you please comment on that approach? Int J Imaging Syst Technol. 2008 Jun 1;18(1):42-68. A METHODOLOGY FOR ANALYZING CU

Re: [Freesurfer] Neonatal Brain

Hi Naama, these brains were manually segmented, then we performed surface-based analysis on them using the manual segmentation. cheers, Bruce On Thu, 3 Dec 2009, Naama Barnea-Goraly wrote: > > Followup to yesterdays question - there is one Freesurfer paper I know > of that did segmentation (an