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

Sun Dec 11 11:25:49 EST 2011

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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