[Mristudio-users] FA values and define ROI

[susumu mori]

Hi Bing,

1) Manual ROI approach
Many papers use manual ROI approach and it's still one of the best ways. The
downside is, you have to be an expert neuroanatomist and even so, the ROI
placement reproducibility is often a concern.

For the manual ROI approach, you can use the DtiStudio "ROI" tab, but I
recommend you to use RoiEditor, which has a much stronger interface.

Using DtiStudio, you need to load an FA map to get FA values. You can
directly draw ROIs on an FA map in the "ROI" tab and determine the average
FA within the ROI. You can also load both color and FA map, draw ROIs on the
color map, and measure FA. In this case, first choose the color map as an
active image in the display in the "Image" tab, go to the "ROI" tab, draw an
ROI, go back to the "Image" tab, choose the FA map as an active image, and
go back to the "ROI" tab to find the FA value.

Using RoiEditor, you need to grasp the concept of "Object", which allows
drawing of multiple 3D ROIs. Our manual is still weak, but you can find some
in www.mristudio.org. There is also a video of our tutorial.

2) Automated ROI
You can use our atlas with more than 170 pre-defined ROIs, warped to your
data. For this approach, you need to get DiffeoMap and RoiEditor from
www.mristudio.org. Also, please read our recent papers by Mori et al, and
Oishi et al, all in NeuroImage. Again, there is online manual in
www.mristudio.org.

3) fiber tracking
Once you successfully segment your brain, you can use the segmented regions
as ROIs for fiber tracking.

#2 and #3 are a bit advanced usage of our tools. #2 could be figured out
through our website, I believe. We are planning to have a tutorial in ISMRM
this year. Hope you can join.

Susumu

On Sun, Feb 28, 2010 at 11:19 PM, <7by3 at queensu.ca> wrote:

> Dear users:
>
> We are doing a DTI project and planning to use DTIstudio. I have some
> questions hope you could help me answer.
>
> 1. How could I define ROI? (we are interested in the DMN brain structures,
> such as medial prefrontal cortex, medial temporal lobe, PCC etc). I just do
> not know how can I find these areas in the brain? Is there anyway that brain
> regions could be marked in the brain? Do I need to use atlas or I can just
> find it from DTI studio? (Hope it makes sense)
>
> 2. I want to get FA values. After clicking tensor, color map etc. tab from
> DTImap. I could not find FA values. Could you let me know how and where to
> find these FA values?
>
> 3. We are also looking at the fiber tract. For example, we want to look at
> the fiber tract from PCC to medial temporal lobe. Therefore, we need to find
> the seed region PCC. But how can I find the location of PCC in the brain?
> (this question is similar to question 1).
>
> Could you help me with these questions?
>
> Thank you!
>
> Bing
>
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