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

Sun Dec 11 11:00:59 EST 2011

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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