Re: [Freesurfer] comparison of mean thickness of gyri in two groups

2009-11-01 Thread Mehul Sampat
Thank you for your suggestions Bruce and Mike. Mike, could you please provide the motivation behind your suggestion of using mean cortical thickness as a covariate ? Let's consider this is the context of a simple example. Let's say we compare the mean thickness of the pre-central gyrus in patien

Re: [Freesurfer] comparison of mean thickness of gyri in two groups

2009-11-01 Thread Michael Harms
To me, it makes much more sense to use mean cortical thickness as a covariate for thickness-based analyses. cheers, Mike H. > Hi Mehul, > > the MNI group had an abstract showing that thickness didn't need eTIV > correction at HBM a number of years ago, and it has been our experience > as well. >

Re: [Freesurfer] Making nice images using FreeSurfer

2009-11-01 Thread Bruce Fischl
Hi Estephan, 1. Can't you just save tiffs of each of the different views and put them together in photoshop? 2. You can write tcl scripts to do this kind of thing. For example make_movie.tcl: read_binary_sulc set min_p 0 set max_p 36 for {set pno $min_p } { $pno <= $max_p} {incr pno 1} {

[Freesurfer] Making nice images using FreeSurfer

2009-11-01 Thread Estephan Moana
Hello FreeSurfer experts, I am playing with displaying FEAT output over the 3D pial surface provided by FS. I was wondering if somebody knows how to: 1. See both hemispheres side-by-side at the same time (both pial and inflated, if possible); 2. Make a video of the output 3D brain rot