Re: [Freesurfer] How to view entire brain results in Freeview for LME data

And now you want to do an ROI analysis or a map-based analysis of the subcortical structures? We don't do the latter as that is a VBM analysis. On 04/08/2016 01:07 PM, Jennifer Legault wrote: > Apologies for likely using the wrong term. I meant to say that I've > done the cluster-thresholding

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

Apologies for likely using the wrong term. I meant to say that I've done the cluster-thresholding for the surface data, using the mri_surfcluster command with annot -aparc as an argument. On Fri, Apr 8, 2016 at 1:03 PM, Douglas N Greve wrote: > This is what I don't

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

This is what I don't understand: "done the cluster-thresholding for the aparc data" The aparc data is an ROI and so you should not have (could not have) done clusterwise thresholding (?) On 04/08/2016 12:57 PM, Jennifer Legault wrote: > Hi Doug, > > I'm currently running the LME

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

Hi Doug, I'm currently running the LME mass-univariate analysis (I've previously conducted the LME univariate analyses with ROIs with little to no problems) and, thanks to your help, have run my data through this analysis and done the cluster-thresholding for the aparc data but not the aseg data

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

On 04/01/2016 04:44 PM, Jennifer Legault wrote: > Hi Doug, > > Thanks for your quick response! When running the LME mass univariate > analysis, I am assuming this also includes subcortical structures, > correct? Which processing are you doing? It should be obvious if you are doing

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

Hi Doug, Thanks for your quick response! When running the LME mass univariate analysis, I am assuming this also includes subcortical structures, correct? From my understanding, subcortical areas are segmented as opposed to parcellated. The main thing I want to examine all the regions of the

Re: [Freesurfer] How to view entire brain results in Freeview for LME data

You can put surface data back into the volume with mri_surf2vol (which will also merge left and right into one volume). What do you do with the aseg data? On 04/01/2016 10:46 AM, Jennifer Legault wrote: > Dear Freesurfer Experts, > > I have run my participants' longitudinal sMRI data through

[Freesurfer] How to view entire brain results in Freeview for LME data

Dear Freesurfer Experts, I have run my participants' longitudinal sMRI data through the preprocessing longitudinal pipeline, ran the LME multivariate analysis, cluster-thresholded the data, and am now trying to visualize those results in Freeview (for some reason tksurfer is very, very slow to