[Mristudio-users] ROI

[susumu mori]

Hi Shaimma,

For anatomical definition, there is no "right" way to define structures
because anatomy doesn't always have clear boundary. It is like a cloud;
very often there is only a gradual transition from one structure to the
other.

I once heard a presentation about a European consortium to try to come up
with a consistent criteria for hippocampus definition and found there was
as much as 100% difference in the hippocampal sizes defined by
neuroanatomists.

When you try to define a structure, like "internal capsule", because WM
often doesn't have clear boundary, you need to come up with a written
protocol to define it based on anatomical landmarks. Then you need to find
intra-rater and inter-rater reproducibility. Your measurements are trusted
only if you present these reproducibility results.

The ROI can be as simple as one ROI in one representative slice. This could
lead to high reproducibility if you choose a slice in which your tract of
interest has clear boundary, but reproducibility could be "0 (meaning no
overlap)" if another person happens to choose a adjacent slice. Also, you
would leave many portion of the tract of your interest unmeasured. The
reproducibility issue could be solved if your protocol says, "first
normalize the brain into the MNI space using affine transformation and
choose axial slice 90".

If your protocol suggests, "all axial slices from the anterior commissure
to the level of the upper boundary of the thalamus in the mid-sagittal
slice", then you may have to define the internal capsule in 10 axial slices.

Again, I'm not saying one is better than the other. Location identification
is the greatest challenge for image analysis and there is no single way to
solve it. Voxel-based analysis can give you automated way with 100%
reproducibility, but it doesn't solve the accuracy problem (can it really
align structures accurately?).




On Sun, Mar 10, 2013 at 1:35 PM, Shaimaa Abdelsattar
<shaimaa96 at hotmail.com>wrote:

> Hi,
> In ROI editor program, if I want to measure FA ,for example in the
> posterior limb of internal capsule, what is the correct method for this ,is
> it  to draw multiple Roi s in all sequential axial planes till i finish it,
> or draw ROI in only few cuts or draw one small  Roi within its substance,
> or all can work?
>
> Thank you very much
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