When I ran the LME mass-univariate analysis as instructed here, doesn't that include subcortical structures?  When I overlay the spval.mgh file from my mass-univariate analyses as an overlay in freeview, I can only see the surface based results; any subcortical structure is in all yellow (please see attached screenshot).  I'm wondering how I can visualize the subcortical results for the LME mass-univariate results. 

Thanks for your help,

Jen


On Fri, Apr 8, 2016 at 1:09 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
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 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
> <greve@nmr.mgh.harvard.edu> wrote:
>> 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 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 (since I'm not sure how to cluster-threshold the
>>> segmented data--any advice you have would be greatly appreciated).  Is
>>> there a way to view the significant voxels overlaid on the
>>> aseg+aparc.mgz in fsaverage for the whole brain?
>>>
>>> Best,
>>>
>>> Jen
>>>
>>> On Fri, Apr 8, 2016 at 12:36 PM, Douglas N Greve
>>> <greve@nmr.mgh.harvard.edu> wrote:
>>>> 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
>>>> surface-based or ROI-based analysis.
>>>>>   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?
>>>> Yes, you can.
>>>>> 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.
>>>> If you are doing an ROI analysis then there is no clustering.
>>>>> 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.
>>>> If you have a value for each ROI (segmentation and/or parcellation),
>>>> then you can read in aseg+aparc.mgz in fsaverage (apas =
>>>> MRIread('aparc+aseg.mgz')), then find all the voxels that belong to a
>>>> given ROI and assign them the value for the ROI, then write it out, then
>>>> view the output as an overlay on orig.mgz
>>>>
>>>>> Best,
>>>>>
>>>>> Jen
>>>>>
>>>>> On Fri, Apr 1, 2016 at 11:23 AM, Douglas N Greve
>>>>> <greve@nmr.mgh.harvard.edu <mailto: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
>>>>>       >
>>>>>       >
>>>>>       > _______________________________________________
>>>>>       > Freesurfer mailing list
>>>>>       > Freesurfer@nmr.mgh.harvard.edu
>>>>>       <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>       > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>       --
>>>>>       Douglas N. Greve, Ph.D.
>>>>>       MGH-NMR Center
>>>>>       greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>>>>       Phone Number: 617-724-2358 <tel:617-724-2358>
>>>>>       Fax: 617-726-7422 <tel:617-726-7422>
>>>>>
>>>>>       Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>>       <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>>>>       FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>>>       www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>>>       <http://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 <mailto: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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>> greve@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
>>>
>> --
>> 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
>> 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
>
>

--
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
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



--
Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University