[Freesurfer] GLM design question

2011-12-10 Thread Martijn Steenwijk
Dear all, I'm relatively new with Freesurfer, but slowly getting more and more used to it's great possibilities. To be 'sure', I've a question about the design of a GLM. I want to compare CT in Healthy Controls vs Diseased, and control for age and sex. It appears to me that factors (eg sex

Re: [Freesurfer] problem with visualizing hippo-subfields

2011-12-10 Thread Koen Van Leemput
Hi Tetiana, Could you please do grep left_CA1 $FREESURFER_HOME/FreeSurferColorLUT.txt and see what the result is? There have been some naming convention changes ("left_CA1 -> left-CA1", etc), so perhaps this is the problem? Thanks, Koen On Thu, Dec 8, 2011 at 7:48 AM, Tetiana Dadakova wrote

Re: [Freesurfer] GLM design question

2011-12-10 Thread Douglas Greve
Yes, that is correct, though I think your matrix should be [.5 .5 -.5 -.5 0 0 0 0]. You should also remove the mean from the age (mean computed from all subjects). Or even better, first test whether there is a group difference in age slope with [0 0 0 0 .5 .5 -.5 -.5]. If there is nothing that

[Freesurfer] Cluster-wise correction for multiple comparisons: customized Zstats data

2011-12-10 Thread Xinian Zuo
Hi List, I have a question on how to write out the matlab vector containing the Z-statistics and perform subsequent multiple corrections. I already read some functions and know how to write it to a mgh surface file. Here, my question is 'is there any specific things on the header of the surface fil