[Mristudio-users] AIR/MI/theory AIR, which is the best?

[susumu mori]

I believe that you can also load the probabilistic maps as an ROI and
calculate the probability-weighted pixel intensity such as FA.

On Sun, Dec 11, 2011 at 11:25 AM, Yajing Zhang <zhangyajing9996 at gmail.com>wrote:

> Hi, Lisa
>
> In case your ROIeditor does not have these probabilistic pathway
> definitions, you can download the files at this page:
> http://lbam.med.jhmi.edu/cmrm/Data_Yajing/fiberMenu.htm . To use them in
> ROIeditor, you can load the data as "raw image".
>
>
> Yajing
>
> On Sun, Dec 11, 2011 at 11:00 AM, susumu mori <susumu at mri.jhu.edu> wrote:
>
>> Hi Lisa,
>>
>> There are multiple terminologies in white matter anatomy and within each
>> terminology, the consensus is not always consistent.
>>
>> In general, there are two different ways to define the white matter
>> anatomy. One is based on the location. For example, "The anterior limb of
>> internal capsule (ALIC)" is a white matter location between the caudate and
>> the putamen.
>>
>> The second way to define the white matter is based on the pathway. In the
>> ALIC, there are corticothalamo and thalamocortical pathways. There are
>> also descending pathways such as cortiopontine, cortiobulbar, and
>> corticospinal tracts.
>>
>> If I pick up, for example, the coritopontine fiber, it starts the motor
>> cortex and go through the peripheral white matter beneath the motor cortex,
>> the corona radiata, the internal capsule, the cerebral peduncle, and the
>> pons. This exemplifies how the same white matter area can be called in
>> different ways.
>>
>> To me, the SLF I, II, and III are more based on pathway definition,
>> connecting different cortical areas.
>>
>> The white matter parcellation maps (PM) we provide are purely based on
>> location information. Therefore, it is quite possible that the
>> pathway-defined structure, such as SLF I not only occupies a portion of the
>> our PM-based SLF and also a portion of SFG-WM.
>>
>> I have to check Xin and Yajing, but the current RoiEditor also contains
>> probabilistic coordinates based on the pathway-based white matter
>> definition. I believe that contains SLF I, II, and III. If your RoiEditor
>> doesn't have these (should be RoiEditor/Images/Tracts), you can find them
>> in our website (lbam.med.jhmi.edu).
>>
>> For the definition of these probabilistic coordinates, please refer to;
>>
>> Zhang YJ, Zhang JY, Oishi K, Faria AV, Jiang HY, Li X, Akhter K,
>> Rosa-Neto P, Pike GB, Evans A, Toga AW, Woods R, Mazziotta JC, Miller MI,
>> van Zijl PCM, Mori S. Atlas-guided tract reconstruction for automated and
>> comprehensive examination of the white matter anatomy. NeuroImage
>> 2010;52(4):1289-1301
>>
>> Xin and Yajing, please let us know where exactly they are.
>>
>> Susumu
>>
>> On Fri, Dec 9, 2011 at 2:07 PM, Lisa Marie Langevin <
>> LisaMarie.Langevin at albertahealthservices.ca> wrote:
>>
>>> Dear Dr. Mori,
>>>
>>> I have been using your atlas to identify and trace the SLF on my
>>> pediatric DTI data.  I am interested in now subdividing the SLF into it's
>>> component parts, but from the literature, it seems as though the ROIs and
>>> tract images don't include the dorsomedial portion of the SLF, known as SLF
>>> I.  SLF II and III figure prominently, however.
>>>
>>> According to the atlas, the region where the SLF I is usually found has
>>> been denoted as superior frontal gyrus white matter (SFG-WM) and superior
>>> parietal gyrus white matter (SPL-WM).
>>>
>>> Is this the most recent terminology?
>>>
>>> This link to a recent Nature article better illustrates the region I am
>>> trying to identify.
>>>
>>> http://www.nature.com/neuro/journal/v14/n10/fig_tab/nn.2905_F1.html
>>>
>>> Thank you!
>>>
>>> Lisa Marie Langevin
>>>
>>>
>>>
>>>
>>>
>>>
>>> Lisa Marie Langevin, PhD.
>>> Postdoctoral Research Fellow
>>> Behavioural Research Unit
>>> Alberta Children's Hospital Research Institute for Child and Maternal
>>> Health
>>> Tel: (403) 955-2785, Fax: (403) 955-2772
>>> Email: lisamarie.langevin at albertahealthservices.ca
>>> ________________________________________
>>> From: mristudio-users-bounces at mristudio.org [
>>> mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori [
>>> susumu at mri.jhu.edu]
>>> Sent: August 11, 2011 5:46 PM
>>> To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
>>> Subject: Re: [Mristudio-users] AIR/MI/theory AIR, which is the best?
>>>
>>> If the scans are not co-registered (the subject went out and came back
>>> to the scanner), I suggest you to calculate the tensor first and register
>>> the tensor using DiffeoMap and linear registration (AIR or MI).
>>>
>>> If you register the raw DWI data, you may get a bit better SNR (this is
>>> my guess), but you have to make sure to use the b-table re-orientation
>>> scheme in the AIR. I would recommend to use AIR or MI (MI may take a lot of
>>> time), although I don't have much experience in the cross-scan registration.
>>>
>>> I think the first method (calculate tensor and then register) is the
>>> easiest.
>>>
>>>
>>> On Thu, Aug 11, 2011 at 6:35 PM, Min Liu <mliu4 at ualberta.ca<mailto:
>>> mliu4 at ualberta.ca>> wrote:
>>>
>>>
>>> Dear MRIStudio users,
>>>
>>> I have four human brain datasets that are scanned sequentially (back
>>> to back) of a single subject using the same DTI protocol. I want to
>>> get an averaged dataset out of the four. Before doing that,
>>> motion/eddy current correction is definitely needed. I am wondering
>>> among the three methods provided by DTIStudio, i.e. AIR/MI?theory AIR.
>>> By visual inspection, there is rotation/shifting between the very
>>> first dataset and the very last by about 2 voxels. For this subtle
>>> movement, is there a conclusion so far regarding which coregistration
>>> is the best (without introducing errors! Sometimes AIR does more harm
>>> than good by misalignment.) Thank you for your thoughts!!
>>>
>>> Min
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>>>
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