[Mristudio-users] ROI

[susumu mori]

Unless you are using tractography-based pixel grouping, you have to visit
every slice to make a 3D ROI.

On Mon, Mar 11, 2013 at 7:23 AM, Shaimaa Abdelsattar
<shaimaa96 at hotmail.com>wrote:

> Thank you very much,
>
> So if I draw 2 ROI s one  at the level A and another one at level B
> (higher by 3 cuts  for example.) using the option (+), to perform 3d ROI as
> you mentioned in tutorial of ROI editor , is the result represents the
> whole volume in between the two cuts or only these 2 cuts individually?, or
> should i draw multiple Rois in each cut in between?
>
> Thanks again
>
> On Mar 11, 2013, at 12:17 PM, "susumu mori" <susumu at mri.jhu.edu> wrote:
>
> 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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