[Mristudio-users] Using ROI for tractography

[susumu mori]

Hi Joanne,

Please see;
Zhang YJ, Zhang JY, Oishi K, Faria AV, Jiang HY, Li X, Akhter K, Rosa-Neto
P, Pike GB, Evans A, Toga AW, Woods R, Mazziotta JC, Miller MI, van Zijl
PCM, Mori S. Atlas-guided tract reconstruction for automated and
comprehensive examination of the white matter anatomy. NeuroImage
2010;52(4):1289-1301. PMC2910162

This paper describes the same idea.
If you want to use WMPM as ROIs, you first have to register it to each
subject.
Assuming the registration is good, you can turn the WMPM into ROIs by the
following procedure;

1) Read the WMPM as an image, not as ROI into RoiEditor
2) By placing the cursor to a pacellated region of interest, you can read
the assigned value. For example, the splenium of the CC is "119".
3) Use the threshold tool and choose pixels with a value "119". This
operation selects all pixels in the splenium of the CC.
4) Register the selected pixels as "Object 1".
5) Repeat the procedure to the second region of interest and register the
selected pixels to "Object 2".
6) Once you define all regions of interest as separate Objects, save the
Objects (the "save" icon in the "ROI" section) as "Binary Map"
7) Read FAQ15 at https://www.mristudio.org/wiki/faq to learn how to use
Binary Map for fiber tracking in DtiStudio. You can combine multiple ROIs
with AND/OR/NOT operations.

For many white matter tracts, we already generated combinations of parcels
defined in the WMPM (e.g. a combination for CST, SLF, etc), which can be
registered to each patient and ready for fiber tracking. I believe these
WMPM-ROI files are posted somewhere in our website. Please contact Yajing
for more detail.

Susumu

On Wed, Nov 9, 2011 at 11:24 PM, Joanne Lin <joanne.lin at auckland.ac.nz>wrote:

>  Hi all,****
>
> ** **
>
> I have a question about saving ROIs from ROIEditor and then using them for
> tractography.****
>
> ** **
>
> I was hoping to perform tractography for each of my participants, but
> because my anatomy knowledge is limited, I wanted to avoid having to
> manually delineating regions.  I have processed the data so the
> JHU_MNI_SS_WMPM_TypeII is in diffusion space; my question is this – is it
> valid to use one (or more) of these atlas-defined structures as ROIs for
> tractography?****
>
> ** **
>
> If so, how can I isolate and save one (or more) of the atlas regions as a
> single ROI on its own?  I have tried ‘hide all’ and unhiding the one/s I am
> interested it but it doesn’t appear to work.  Apart from deleting all of
> the (many) structures I’m not interested in, is there a way to do this
> properly?****
>
> ** **
>
> Also, is ‘binary map’ the best format to save ROIs to use in fibre
> tracking?****
>
> ** **
>
> Any advice greatly appreciated.  Thank you kindly for your help!  ****
>
> ** **
>
> Kind regards,****
>
> Jo****
>
> ** **
>
> ** **
>
> *Joanne Lin*
>
> BPharm (Hons), RegPharmNZ****
>
> ** **
>
> Pharmacist/PhD Candidate
> School of Pharmacy****
>
> Faculty of Medical & Health Sciences****
>
> The University of Auckland****
>
> Private Bag 92019****
>
> Auckland, New Zealand****
>
> +64 9 373 7599 Ext 88468****
>
> ** **
>
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