[Mristudio-users] ROI

[Dorian P.]

Dr. Mori, would you advise to overlay the white matter atlas and obtain
regional FAs that way? If not, why?

I am aware that tracts change in each person, but sounds the best way to
categorize FA regions without going for tractography.

Dorian

2013/3/11 susumu mori <susumu at mri.jhu.edu>

> 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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