[Freesurfer] one factor with three levels in qdec?

Dear FreeSurfer creators and experts, I am trying to run qdec with one discrete with three levels (i.e., https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error message: ERROR: no contrasts specified. Error in Analyze: command failed: mri_glmfit --y … I am wondering if

Re: [Freesurfer] one factor with three levels in qdec?

sorry, you cannot have three levels in qdec (two max). You will need to use the command line stream (ie, create a FSGD file and consrast files, run mris_preproc, mri_surf2surf to smooth, mri_glmfit, and mri_glmfit-sim). See the wiki for more details. doug On 2/16/14 4:53 PM, Yang, Daniel

Re: [Freesurfer] one factor with three levels in qdec?

Hi Doug, Thanks, I see. That really helps a lot. I will try to use the command line version. Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 2/16/14 7:13 PM, Douglas Greve

[Freesurfer] Interaction test

Dear FreeSurfer developers and experts, If I have a binary factor (Group1: patients, Group2: controls) and a continuous variable (age), I know I can follow Contrast2 in the following wiki to test the interaction effect. http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V Contrast2: [0 0 1

[Freesurfer] Which is broken - GCC or Freesurfer build?

Hi Freesurfer experts, so I got this error when I ran recon-all on my cluster. I am really hoping this is just a case of missing GCC libraries and nothing is wrong with the Freesurfer installation on the nodes. Kindly confirm this. Thank you