Re: [Freesurfer] contrast matrix for 2 discrete factors and 3 continuous variables

Hi Jose, with 6 classes and 3 continuous variables, I think you should have 24 regressors, which means 24 columns in the contrast matrix. Yours only has 18. Otherwise the contrast to test between B and C is correct (just need to add 6 zeros). For the interaction, you would need 0 0 0.5 -0.5 -0.

Re: [Freesurfer] mkanalysis-sess -gui

what is the error? Why are you using version 4 instead of 5? Version 5 solves the problem by not having a GUI:). doug Iris.steinmann wrote: > Hi Freesurfers, > > I have a little problem: I use a linux mashine with ubuntu 10.10 and > installed freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz..

[Freesurfer] Converting nii to label....

Hi, I have a volume in .nii format which I would like to use as an ROI to extract signal from, using func2roi-sess. However, func2roi requires a label. How would I convert a .nii volume to a label? Thanks, Joe Andreano _ Joseph M. Andreano, PhD Postdoctoral Re

Re: [Freesurfer] Converting nii to label....

Use mri_cor2label (it is a badly named program). doug Joseph Andreano wrote: > Hi, > > I have a volume in .nii format which I would like to use as an ROI to > extract signal from, using func2roi-sess. However, func2roi requires a > label. How would I convert a .nii volume to a label? > > Thanks

Re: [Freesurfer] contrast matrix for 2 discrete factors and 3 continuous variables

Thanks Doug for your reply. I forgot that the number of columns is number of classes by number of covariates +1. So, I only want you to confirm me that the extra zero that I've seen in the FSwiki example is an erratum (see contrasts 7 and 8 in Four Groups (2 Factors, Two Levels), One Covariate

Re: [Freesurfer] contrast matrix for 2 discrete factors and 3 continuous variables

yep, those are typos. I just fixed them. thanks doug Jose Luis Cantero Lorente wrote: > Thanks Doug for your reply. I forgot that the number of columns is > number of classes by number of covariates +1. > > So, I only want you to confirm me that the extra zero that I've seen > in the FSwiki exam

[Freesurfer] How to make a surface overlay? - repost

Hi, I've done some statistics on thickness and volume of the default cortical regions (segIDs 1000 - 1035 and 2000 - 2035) for a number of subjects. How can I show for instance the p values (expressed as -log(p)) as an overlay on the pial surface of fsaverage? Ed

[Freesurfer] New Random Field Theory tool specifically for Freesurfer-based data analyses

Dear freesurfers I have uploaded to the NITRC neuroimage database a new tool called RFT_FDR. This tool implements Random Field Theory and Hierarchical multiple comparison corrections specifically for Freesurfer's surface data. The tool depends on Worsley´s SurfStat toolbox which is already incl

[Freesurfer] Segmentation Fault Question

Hi, I am accessing my subject directory on a network attached drive. When I run mri glmfit it segfaults. However, it works if the subject directory is on my own computer. Do you have any way to do this with the subject directory on the network drive? Below is a sample output. Thanks, Allie Cadu

Re: [Freesurfer] Segmentation Fault Question

It's dying when creating the output directory. Does the output dir get created? If not, do you have write permissions to that dir? doug Allie Rosen wrote: > Hi, > > I am accessing my subject directory on a network attached drive. When > I run mri glmfit it segfaults. However, it works if the su