On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve <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

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>> 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>> 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>
>>
>>
>> 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>>> 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>
>> Phone Number: 617-724-2358 <tel:617-724-2358>
>> Fax: 617-726-7422 <tel:617-726-7422>
>>
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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

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