On Tue, Nov 1, 2016 at 5:22 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

You can certainly get the lh and rh ROI stats in table form and then do
an asymmetry analysis. Or you can use the xhemi stream to do a
vertex-wise analysis. the difference is the difference between ROI and
map-based analysis

On 11/01/2016 03:47 PM, Daya P wrote:
> Thank you a lot!
>
> I will try this. I had another question regarding statistical analysis
> for asymmetry. I have seen several papers that take the measures that
> come from freesurfer (i.e. cortical thickness of auditory cortex), and
> use MATLAB or SPSS to run statistical tests.
>
> I am looking at 13 regions in each hemisphere and want to check for
> asymmetry across 9 participants. Is there a way to do this within
> Freesurfer?
> Otherwise, I am still looking into what the most appropriate test and
> post hoc test would be. From asking several people there doesn't seem
> to be a straight answer.
>
> Thank you,
> Daiana
>
> On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> I've written a script that will come out with version 6, but I've
> put it
> here
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
> <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas>
>
> I think it should work in 5.3, but I'm not sure. If not, you can
> download the dev version and make the atlas using that. Run it with
> --help to get info on how to run it.
>
>
>
> On 10/28/2016 05:10 PM, Daya P wrote:
> > Hi Doug,
> >
> > I needed to make a registration template and an cortical atlas
> because
> > I am trying to measure cortical thickness, GM and surface area
> on cat
> > brains.
> >
> > What would be the necessary changes?
> > Would it be possible (and appropriate) to use just
> > mris_left_right_register instead?
> >
> > Daiana
> >
> > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > A difference of 10 out of 500 or 1000 does not both me at
> all. Why
> > do you need to create your own atlas? It is doable for the cross
> > hemi stuff, it is just difficult.
> >
> >
> > On 10/26/16 10:16 AM, Daya P wrote:
> >>
> >> Thank you for your help!
> >>
> >> I created a registration template and atlas from scratch
> could I
> >> input that in the interhemispheric registration analysis?
> >>
> >> The ROIs for the diffrerent regions per hemisphere are 50-100
> >> vertices
> >>
> >> On Oct 24, 2016 5:03 PM, "Douglas N Greve"
> >> <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu

> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >>
> >> It would depend on how big the ROI is to begin with. Do you
> >> know that we
> >> have our own interhemispheric analysis that might be better
> >> for this?
> >> Check out
> >>
> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>
> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>>
> >>
> >>
> >> On 10/24/2016 12:33 PM, Daya P wrote:
> >> > Hi Bruce,
> >> >
> >> > I drew ROIs on an initial subject and then after
> >> registering all other
> >> > subjects to the initial one, used mri_label2label to map
> >> the ROIs from
> >> > the initial subject to subsequent ones.
> >> > I am interested in looking at asymmetry between left and
> >> right regions.
> >> >
> >> > I had two concerns, one that the ROIs have different #
> >> vertices on
> >> > different subjects, but as you mentioned the nonlinear
> >> process makes
> >> > sense, since each subject does not have the exact same
> >> brain size and
> >> > curvature.
> >> >
> >> > Another concern was that the ROIs on the left and right
> >> hemisphere in
> >> > a subject do not have the exact same number of vertices.
> >> Would a
> >> > difference of 10 vertices max bias results?
> >> >
> >> > Thank you for your help,
> >> >
> >> > Daiana R. Pur
> >> > Research Assistant
> >> > Canadian Surgical Technologies & Advanced Robotics
> >> > Brain and Mind Institute
> >> > Western University
> >> > London, ON, N6A 5B7
> >> > Canada
> >> >
> >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl
> >> > <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> >> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>
> >> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> >> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote:
> >> >
> >> > Hi Daiana
> >> >
> >> > yes, that is to be expected given the nonlinear
> nature
> >> of the
> >> > cross-subject registration. It shouldn't bias things,
> >> although
> >> > you'll need to give us more details if you want a
> more
> >> definitive
> >> > answer.
> >> >
> >> > cheers
> >> > Bruce
> >> >
> >> >
> >> >
> >> > On Mon, 24 Oct 2016, Daya P wrote:
> >> >
> >> > Hi All,
> >> >
> >> > My question is about using mri_label2label. When
> >> mapping the
> >> > labels from one
> >> > subject to another the number of vertices of each
> >> ROI is
> >> > different. Is that
> >> > something to be expected?
> >> >
> >> > How much of a difference does a number of
> vertices
> >> of 50
> >> > compare to 40 have
> >> > on measures like thickness, grey matter and
> surface
> >> area?
> >> >
> >> > I would really appreciate some help
> >> >
> >> > Thank you,
> >> >
> >> > Daiana R. Pur
> >> > Research Assistant
> >> > Canadian Surgical Technologies & Advanced
> Robotics
> >> > Brain and Mind Institute
> >> > Western University
> >> > London, ON, N6A 5B7
> >> > Canada
> >> >
> >> >
> >> >
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> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
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> >>
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> --
> 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>
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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