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 brain that might change over time (as a function of the training task I've given my participants), so I would look at both the aparc and the aseg data, right?   Apologies if I've misunderstood your question.  For the aseg data, I am currently having trouble with figuring out how to cluster threshold the data (do i use mri_surfcluster with an argument to call the aseg annotation or do I use mri_volcluster?) I would then want to visualize the cluster thresholded data for subcortical structures in freeview.   Optimally, I would like to find some way to look at the whole brain in Freeview to see these regions that have changed as a function of my training task.  

Best,

Jen

On Fri, Apr 1, 2016 at 11:23 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
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 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 run on my computer).  I am interested in the Fs volume
> (thickness*area) measure.
>
> I noticed in the FsFast Tutorial
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel>,
> that all the corrected results were able to be merged into one file
> using the vlrmerge command.  In the beginning of the tutorial, it
> states that fMRI and structuraI group analyses run similarly. / I was
> therefore wondering if I can use the vlrmerge command (or some similar
> command) for my LME data, such that I can view the following
> information all in one file: both hemispheres, aparc and aseg.
> / Currently I can only view the aparc results for each of the
> hemispheres separately (and I haven't found a way to visualize the
> aseg data).
>
> Thank you for taking the time to read this email.
>
> Best,
>
> Jennifer Legault
> Ph.D candidate, Neuroscience
> Brain, Language, and Computation Lab
> The Pennsylvania State University
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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--
Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University