[Mristudio-users] WMPM

[susumu mori]

You need to use DiffeoMap first to warp your data to our atlas or warp the
atlas to your data.
Then RoiEditor can superimpose WMPM for automate WM parcellation.

You can find Video Tutorial here (https://www.mristudio.org/wiki/user_manual
).
Getting Started here (https://www.mristudio.org/wiki/user_manual/diffeomap)
should also help.

I think you need your own normal data for control.

On Thu, Mar 7, 2013 at 12:23 AM, Shaimaa Abdelsattar
<shaimaa96 at hotmail.com>wrote:

> Thank you, it is now clear for me.
> I have another question, how can I superimpose white matter PM into my
> subjects.
> Another question please, can I use one of the atlas templates as a control
> to my subjects in my research.
>  thanks
>
> On Mar 7, 2013, at 5:01 AM, "susumu mori" <susumu at mri.jhu.edu> wrote:
>
> The best way is to download the latest RoiEditor.
> Our atlas is evolving and now we have version numbers.
>
> On Wed, Mar 6, 2013 at 9:59 PM, Raag Airan <rairan1 at jhmi.edu> wrote:
>
>> Hello all,
>>
>> Where could I find an up to date listing of the which regions correspond
>> to each ROI of the atlases - specifically with regard to the Brain
>> Parcellation Maps?
>>
>> Thanks,
>> Raag
>>
>>
>> On Wed, Mar 6, 2013 at 9:56 PM, Susumu Mori <susumu at mri.jhu.edu> wrote:
>>
>>>  There are several types of WMPM. Actually our newer version of
>>> parcellation maps include gray matter structures too.
>>> So, we are now calling it Brain Parcellation Maps (BPM).
>>>
>>>  There are two type of parcellation maps; population-averaged and
>>> single-subject.
>>>
>>>  ICBM-DTI-81 atlas is a population-averaged atlas, which has WMPM.
>>> Because it is a population map, it is not a real brain. After averaging 81
>>> subjects, many structures with high anatomical variability smeared out and
>>> not definable anymore. For example, the fine white matter branches into the
>>> cortex disappear. Therefore, we can define only the core of the white
>>> matter. The WMPM contains structural definitions of only these core WM
>>> regions.
>>>
>>>  In the averaged FA/color maps, you can clearly see core WM structures
>>> like the internal capsule. We manually defined these structures. As you
>>> approach to the cortex, we find pixels which are 100% WM in all 81 subject
>>> as well as pixels which are only 50% WM (WM in 40 subjects and other 40
>>> subjects are the cortex). We can threshold the population averaged map at
>>> 90, 80, 70, and 60%. As the % goes up, the defined WM shrinks. If you
>>> superimpose one of the WM structures with 90% threshold on your subjects
>>> (of course, after normalization), it is highly likely that this ROI defines
>>> almost pure WM with a small contamination of the cortex.
>>>
>>>  Does it make sense?
>>>
>>>
>>> On Wed, Mar 6, 2013 at 10:59 AM, Shaimaa Abdelsattar <
>>> shaimaa96 at hotmail.com> wrote:
>>>
>>>> Hi,
>>>> Could you please tell me the difference between the different types of
>>>> WMPMs. I found what is called WMPM 80 % or etc.....
>>>>
>>>> Thanks
>>>>
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>>>
>>
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