[Freesurfer] questions about group analysis

2006-08-25 Thread Ray Fix
Hello, I have some questions about doing group analysis. I know these are really basic... but everyone loves easy softballs, right? Question 1. How should I define multiple classes? The tutorial examples show two classes, male and female. If I have patient and controls, in addition to m

Re: [Freesurfer] visualizing surfaces

2006-08-25 Thread Dahlia Sharon
for BEMs it'll work... On Fri, 25 Aug 2006, Bruce Fischl wrote: only if they have the same # of faces/vertices though. Scuba is much more general. On Fri, 25 Aug 2006, Dahlia Sharon wrote: Hi Camilo, You can load a 3rd surface by going to: File > Aux Surface > Load Aux Surface Configuration

Re: [Freesurfer] visualizing surfaces

2006-08-25 Thread Bruce Fischl
only if they have the same # of faces/vertices though. Scuba is much more general. On Fri, 25 Aug 2006, Dahlia Sharon wrote: Hi Camilo, You can load a 3rd surface by going to: File > Aux Surface > Load Aux Surface Configuration > Pial Vertices and then choosing whatever surface you want (doesn

Re: [Freesurfer] visualizing surfaces

2006-08-25 Thread Dahlia Sharon
Hi Camilo, You can load a 3rd surface by going to: File > Aux Surface > Load Aux Surface Configuration > Pial Vertices and then choosing whatever surface you want (doesn't have to be pial, can be a BEM). Dahlia. On Fri, 25 Aug 2006 [EMAIL PROTECTED] wrote: Hi Freesurfer, Is there a way to

Re: [Freesurfer] visualizing surfaces

2006-08-25 Thread Bruce Fischl
in tkmedit? Try using scuba instead On Fri, 25 Aug 2006 [EMAIL PROTECTED] wrote: Hi Freesurfer, Is there a way to visualize 3 surfaces at the same time. I am trying to visualize the BEMs in my flash directory. So far, I can only load 2 of them by loading the main surface and the axiliar surfac

[Freesurfer] visualizing surfaces

2006-08-25 Thread camilo
Hi Freesurfer, Is there a way to visualize 3 surfaces at the same time. I am trying to visualize the BEMs in my flash directory. So far, I can only load 2 of them by loading the main surface and the axiliar surface. Thanks, Camilo ___ Freesurfer mailin

Re: [Freesurfer] preprocessing question

2006-08-25 Thread Doug Greve
Which way do you want to go? Convert FS volumes back into the native space or the other way around? To convert native space vols into FS, run something like: tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat This will bring up both the conformed and nonconf volumes

[Freesurfer] preprocessing question

2006-08-25 Thread Goldman, Aaron (NIH/NIMH) [C]
Hi, I have a few datasets I ran in freesurfer that were originally in 181x217x181 format. As usual, these were converted to 256^3 early in the process. Basically, I'd like to run some comparison stats between the freesurfer volumes and the same subjects run in a couple other programs (that are stil

[Freesurfer] new feature for glmfir/fsgd

2006-08-25 Thread Doug Greve
I've added a new feature to the FreeSurfer Group Descriptor (FSGD) file which allows you to easily use the volume subcortical structures as covariates in a mri_glmfit analysis. An example is: GroupDescriptorFile 1 Title test Class main VariableFromASeg Left-Hippocampus Variables

Re: [Freesurfer] mris_preproc and thickness

2006-08-25 Thread Doug Greve
If you use "--meas xyz" it's going to look for lh.xyz, so you can spec anything as long as it is a curv format or volume-encoded surface value file. Sasha Wolosin wrote: Dear all, Does "--meas thickness" as an input for mris_preproc always specify to use the ?h.thickness file in the surf

[Freesurfer] mris_preproc and thickness

2006-08-25 Thread Sasha Wolosin
Dear all, Does "--meas thickness" as an input for mris_preproc always specify to use the ?h.thickness file in the surf folder? Is there a way to specify a different thickness file as input for mris_preproc? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Pro