Hi Lisa,<div><br></div><div>There are multiple terminologies in white matter anatomy and within each terminology, the consensus is not always consistent.</div><div><br></div><div>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. </div>
<div><br></div><div>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. </div>
<div><br></div><div>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.</div>
<div><br></div><div>To me, the SLF I, II, and III are more based on pathway definition, connecting different cortical areas.</div><div><br></div><div>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.</div>
<div><br></div><div>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 (<a href="http://lbam.med.jhmi.edu">lbam.med.jhmi.edu</a>). </div>
<div><br></div><div>For the definition of these probabilistic coordinates, please refer to;</div><div><br></div><div><span style="font-size:11.0pt;font-family:"Times New Roman","serif"">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</span></div><div><br></div><div>Xin and Yajing, please let us know where exactly they are.</div><div><br></div><div>Susumu<br><br><div class="gmail_quote">On Fri, Dec 9, 2011 at 2:07 PM, Lisa Marie Langevin <span dir="ltr"><<a href="mailto:LisaMarie.Langevin@albertahealthservices.ca">LisaMarie.Langevin@albertahealthservices.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Dr. Mori,<br>
<br>
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.<br>
<br>
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).<br>
<br>
Is this the most recent terminology?<br>
<br>
This link to a recent Nature article better illustrates the region I am trying to identify.<br>
<br>
<a href="http://www.nature.com/neuro/journal/v14/n10/fig_tab/nn.2905_F1.html" target="_blank">http://www.nature.com/neuro/journal/v14/n10/fig_tab/nn.2905_F1.html</a><br>
<br>
Thank you!<br>
<br>
Lisa Marie Langevin<br>
<br>
<br>
<br>
<br>
<br>
<br>
Lisa Marie Langevin, PhD.<br>
Postdoctoral Research Fellow<br>
Behavioural Research Unit<br>
Alberta Children's Hospital Research Institute for Child and Maternal Health<br>
Tel: <a href="tel:%28403%29%20955-2785" value="+14039552785">(403) 955-2785</a>, Fax: <a href="tel:%28403%29%20955-2772" value="+14039552772">(403) 955-2772</a><br>
Email: <a href="mailto:lisamarie.langevin@albertahealthservices.ca">lisamarie.langevin@albertahealthservices.ca</a><br>
________________________________________<br>
From: <a href="mailto:mristudio-users-bounces@mristudio.org">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org">mristudio-users-bounces@mristudio.org</a>] On Behalf Of susumu mori [<a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>]<br>
Sent: August 11, 2011 5:46 PM<br>
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support<br>
Subject: Re: [Mristudio-users] AIR/MI/theory AIR, which is the best?<br>
<div class="im"><br>
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).<br>
<br>
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.<br>
<br>
I think the first method (calculate tensor and then register) is the easiest.<br>
<br>
<br>
</div><div class="im">On Thu, Aug 11, 2011 at 6:35 PM, Min Liu <<a href="mailto:mliu4@ualberta.ca">mliu4@ualberta.ca</a><mailto:<a href="mailto:mliu4@ualberta.ca">mliu4@ualberta.ca</a>>> wrote:<br>
<br>
<br>
Dear MRIStudio users,<br>
<br>
I have four human brain datasets that are scanned sequentially (back<br>
to back) of a single subject using the same DTI protocol. I want to<br>
get an averaged dataset out of the four. Before doing that,<br>
motion/eddy current correction is definitely needed. I am wondering<br>
among the three methods provided by DTIStudio, i.e. AIR/MI?theory AIR.<br>
By visual inspection, there is rotation/shifting between the very<br>
first dataset and the very last by about 2 voxels. For this subtle<br>
movement, is there a conclusion so far regarding which coregistration<br>
is the best (without introducing errors! Sometimes AIR does more harm<br>
than good by misalignment.) Thank you for your thoughts!!<br>
<br>
Min<br>
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