[Freesurfer] strange result in qdec and mri_glmfit

Dear Freesurfer experts, I've just finished running a qdec analysis of a comparison of cortical thickness between controls and patients with 2 covariates and found a strange result. When i set the threshold at FDR some clusters appear in red which are the corrected results from my analysis. Howev

Re: [Freesurfer] Creating a label

This is something that happens when you go back and forth between the volume and the surface (ie, it is not necessarily reversible). It is better to stay within the surface if you can. doug liang wang wrote: > Hi, > > I can create a label file from either ?h.aparc.annot (using > mri_annotation

Re: [Freesurfer] strange result in qdec and mri_glmfit

Sounds like something when wrong. Can you tar up the qdec output directory and drop it to me at the file drop below? doug Joana Braga Pereira wrote: > > > Dear Freesurfer experts, > > I've just finished running a qdec analysis of a comparison of cortical > thickness between controls and patie

[Freesurfer] Freesurfer failure with diseased brains

Hi, I've been using Freesurfer's 'recon-all' function to process T1 datasets of healthy age-matched, MCI and early-onset Alzheimer's brains. It has been successful with the two healthy controls I've tried, but only half of the MCI and EAD brains work - Freesurfer fails and exits 'with errors'.

Re: [Freesurfer] Freesurfer failure with diseased brains

Hi Heather you need to let us know what exactly is failing, and what version of FS you are running. We have run it on a ton of early AD subjects without much trouble. cheers Bruce On Thu, 22 Jul 2010, H. Reynolds wrote: > Hi, > > I've been using Freesurfer's 'recon-all' function to process T

[Freesurfer] Registration with fsaverage

Hi Freesurfers, I am trying to check the spherical alignment of an individual subject registered to fsaverage via lh.sphere.reg. I am using the following command in tksurfer: tksurfer CL lh sphere and get the error code below. Could someone let me know what I am missing here? Should I be using t

Re: [Freesurfer] Registration with fsaverage

Hi Corey usually that means you recreated one of the surfaces without regenerating the other. Try running recon-all -make all -s CL and see if it rebuilds some files On Thu, 22 Jul 2010, Corey Keller wrote: > Hi Freesurfers, > > I am trying to check the spherical alignment of an individual subj