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 <gr...@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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University
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