[Freesurfer] Extracting contrast data from mri_glmfit to graph

External Email - Use Caution Hello, I have a question regarding how to graph results that came from a vertex wise analysis using the command mri_glmfit and mri_glmfit-sim. I was interested in investigating an interaction effect between groups and my variable of interest

Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

External Email - Use Caution Hi Douglas, thanks for your response. >They should not, but the reason it fairly convoluted. When you get a >cluster after running mri_glmfit-sim, that cluster is on fsaverage which >is an average of 40 subjects. The area of a vertex is computed as

Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

explicitly > do so (though it generally does not stop anyone:). > > > > On 9/8/2019 7:37 PM, cody samth wrote: > > External Email - Use Caution > Hi Douglas, thanks for your response. > > >They should not, but the reason it fairly convoluted. When you get

[Freesurfer] Freesurfer three groups: group A vs C power.

External Email - Use Caution Hi I have a question regarding how freesurfer calculates the degrees of freedom when you have three groups in the FSGD/contrast files but are running analyses on group A vs C. For example I have an analysis with 3 groups and 2 covariates. My primary

[Freesurfer] Freesurfer analyses in MATLAB

External Email - Use Caution Hi I'm interested in running some analyses in matlab using freesurfer commands. I'm running an interaction effect, however I'm having issues residualizing the brain values to plot. For running interaction effects I'm running it by inputting:

Re: [Freesurfer] Reporting Results in a three group analysis

eraging over a group of vertices. I guess you > could constrain your post-hoc analysis to be within the main effect > cluster; that would be most consistent. But I don't think you'd have any > problems getting it published either way. > > On 12/2/2019 3:12 PM, cody samth wrote: >

Re: [Freesurfer] Reporting Results in a three group analysis

External Email - Use Caution Thanks for the help! On Wed, Dec 4, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Yes, but threshold it first, eg > mri_binarize --abs --i sig.cluster.mgh --min .01 --o newmask.mgh > > On 12/4/19 1

[Freesurfer] Group effect Contrast for 6 groups

External Email - Use Caution Hi, I'm designing an analysis that will have 6 groups (two factors/three levels). I was wondering if I could get some input regarding my contrast for the group effect. Based on the group effect contrast under the FSGD examples for 3 groups I've

Re: [Freesurfer] Group effect Contrast for 6 groups

hich is what you > are testing. The other contrasts are redundant (and would cause an error if > you added them to the contrast matrix)z > > On 10/16/19 12:03 PM, cody samth wrote: > > External Email - Use Caution > Hi, > > I'm designing an analysis that will ha

[Freesurfer] Reporting Results in a three group analysis

External Email - Use Caution Hi, I have a statistical question about how to approach reporting results from FreeSurfer analyses containing three groups. I ran a group effect (F-test) and then post-hoc tests looking at pair-wise comparisons between the three groups. My question is

[Freesurfer] Creating a label from overlapping cluster results

External Email - Use Caution Hi, I was wondering if there is any automated command/method to create a new label that consists of the overlap of two labels? I've run two whole brain analyses with different predictors and have regions where the clusters from each analysis overlap.