[Freesurfer] Fwd: Error with experimental design using FSGD

Hello Sir/Madam, I am currently running a statistical test using the FSGD method. I am encountering a problem in relation to the creation of the glmdir folder when I run the mri_glmfit function. I recieve an ERROR message that tells me that the design matrix (automatically generated) is ill condit

[Freesurfer] Issues with Cluster generation

Hello all, I am facing a problem whereby after running GLMfit and cluserwise correction for multiple comparisons using the monte-carlo method, I was unable to generate any clusters. I do have significant images produced for the glmfit. All procedures were done according to the tutorial to match t

[Freesurfer] mri_glmfit files

Hello all, I would just like to know what is the significance of the files that are produced after a glmfit is done. I was trying to find a write up online but I was not able to. They include : - cnr.mgh - F.mgh - gamma.mgh - gammavar.mgh - sig.mgh Thank you

[Freesurfer] Cortical thickness

Hello everyone, Please pardon my rather simple question I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares

Re: [Freesurfer] Cortical thickness

be a file called something like cache.th13.abs.y.ocn.dat. > This will have a column for each cluster and a row for each subject. The > value in the row will be the input for each subject. > doug > > On 05/30/2013 11:21 PM, Joshua deSouza wrote: > > Hello everyone, > &g

Re: [Freesurfer] Cortical thickness

mri_glmfit-sim. It might be named something > different depending on your parameters (should always end in y.ocn.dat) > doug > > > On 6/2/13 3:57 AM, Joshua deSouza wrote: > > Hi Doug, > > This file that your saying, will be created after glmfit-sim is done > using the

Re: [Freesurfer] Cortical thickness

he input? cortical thickness? Are you using your own mask or is this a > whole hemisphere analysis? > > doug > > > > > > > On 6/2/13 10:29 PM, Joshua deSouza wrote: > > Hello Doug, > > Thank you for your quick replies to my queries. Really appreciate it.

Re: [Freesurfer] Cortical thickness

n Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza wrote: > Hello Doug, > > Each individuals subject data has already been smoothed by 5 10 15 20 and > 25 through the qache function during the initial processing. > > I'm a little confused now. I thought that the mri_preproc

Re: [Freesurfer] Cortical thickness

at 12:16 AM, Douglas N Greve wrote: > Unless you specify otherwise, mris_preproc will use unsmoothed data. If > you then smooth it with mri_surf2surf and run run mri_glmfit with --fwhm > then you will be smoothing it twice. > doug > > > > > On 06/04/2013 09:49 PM, Joshu

Re: [Freesurfer] Cortical thickness

, Douglas N Greve wrote: > > I think when you smooth it that much strange things happen. Try just one > smoothing of 15mm. > > > > > On 06/06/2013 03:36 AM, Joshua deSouza wrote: > >> Hi Doug, >> >> I did not specify anything in the mris_preproc, so it would be

[Freesurfer] Editing masks

Hello all, I am having a problem with generating values of the vertices at the hippocampal area. I believe it is a masking issue as reviewing the mask after the glmfit analysis I see that the mask does not cover the entire medial region excluding the corpus callosum. Can I do anything to change th

Re: [Freesurfer] Editing masks

achieve? > > cheers > Bruce > > On Tue, 11 Jun 2013, Joshua deSouza wrote: > > Hello all, >> >> I am having a problem with generating values of the vertices at the >> hippocampal area. I believe it is a masking issue as reviewing the mask >> after the glmfit