Re: [Freesurfer] FDR Correction of NHP Surface Data

Thanks Michael, I'll look into Nipy's FDR tools. I actually started this thread asking for help getting mri_surfcluster running for my situation (I have no talraich .xfm and no segmentation for my monkeys). The silence on that topic suggest that it might not be possible, or it's at least not k

Re: [Freesurfer] creating a gca file from .mgz files

i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt n

Re: [Freesurfer] FDR Correction of NHP Surface Data

Hi Clark, If you're loading the data into Python anyway to use with PySurfer, Nipy seems to have some utilities to do an FDR correction (docs /source

Re: [Freesurfer] freeview tracula error

Thank you for the almost immediate reply. Yes, it seems to be otherwise working, cheers, Cat From: Nick Schmansky To: Cat Chong Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, August 29, 2012 2:35 PM Subject: Re: [Freesurfer] freeview tracula error

Re: [Freesurfer] freeview tracula error

does freeview otherwise appear to be working? that is, does it crash? the 'invalid drawable' messages can be ignored on the mac. n. On Wed, 2012-08-29 at 14:29 -0700, Cat Chong wrote: > > Dear Experts: > I have worked my way through Tracula and things seem to work fine, but > when I try to

[Freesurfer] freeview tracula error

  Dear Experts: I have worked my way through Tracula and things seem to work fine, but when I try to view my tractography outputs I get the following persistent error using freeview (copied below). I am using a Mac OS X 10.6.7. freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Could this

Re: [Freesurfer] creating a gca file from .mgz files

Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz

[Freesurfer] Loading nifti overlays with TCL script

Hello Freesurfers, I have a basic question as I'm just getting into scripting, but I'm trying to write a script that loads overlays from multiple contrasts and takes images. However, I can't figure out how to properly load nifti files as overlays. I'm attempting to load .nii volumes from group lev

Re: [Freesurfer] mri_watershed and other errors.

try running: recon-all -s -skullstrip -no-wsgcaatlas if that works, continue the rest with: recon-all -s -autorecon2 -autorecon3 n. On Wed, 2012-08-29 at 17:01 +, Darren R Gitelman wrote: > Hi > > I am having a problem getting recon-all to finish on 1 subject. > > The first time I r

Re: [Freesurfer] FDR Correction of NHP Surface Data

Hi Sebastian, I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model. At the very least, is there any way to automat

[Freesurfer] contrast matrix

Hi Freesurfers, My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M) So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. Then I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regress