<div dir="ltr">Dear Susumu,<div><br></div><div>Thank you for the advice. I have extracted the ROIs from the JHU parcellation atlas. Now, I am using MRICro in order to extract FA values for all the patient data for the ROIs where I would note the min,mean and max values of FA for all ROIs. But is there are way where I could automatically get my FA values for all the subjects for a specific ROI into a .txt file.</div>
<div><br></div><div>Please let me know at your convenience.</div><div>Thank you for your time and consideration.</div><div>Thanks and regards,</div><div>Ravi</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Sat, Aug 17, 2013 at 5:36 PM, Susumu Mori <span dir="ltr"><<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">To make our parcellation map overlapped well on your data, you need to use our LDDMM-based non-linear image alignment. If this cannot align the parcellation map, then, you need to improve the LDDMM results.<div>
<br></div><div>Usually, following steps help;</div><div>> use both FA and MD (or trace) map to drive the LDDMM</div><div>> segment the ventricles and use them for the third channel of LDDMM</div></div><div class="HOEnZb">
<div class="h5"><div class="gmail_extra">
<br><br><div class="gmail_quote">On Sat, Aug 17, 2013 at 4:00 AM, Kotikalapudi Raviteja <span dir="ltr"><<a href="mailto:raviteja.kotikalapudi@gmail.com" target="_blank">raviteja.kotikalapudi@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Susumu,<div><br></div><div>I have been using JHU-Parcellation atlas for DTI analysis. I want to extract the FA maps from corticospinal tract for which I made an ROI from the JHU-Parcellation atlas. But it is not overlapping well with the FA images. I need to know if there is a way to shift the ROI on the FA image?</div>
<div><br></div><div>Your suggestions would be appreciated.</div><div><br></div><div>Many thanks,</div><div>Ravi</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Aug 16, 2013 at 11:03 PM, Susumu Mori <span dir="ltr"><<a href="mailto:smoriw@gmail.com" target="_blank">smoriw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Ying,<div><br></div><div>Here is my view of "registration".</div><div><br></div><div>> Imaging is all about what is where.</div>
<div>> When you quantify images, you have to make sure that you are measuring the same structures or locations across subjects. This act of identifying the same thing is "registration".</div>
<div>> For example, you can manually define the hippocampus across subjects. By doing so, you identify a group of voxels that belong to the hippo and you "register" the hippo locations across subjects. You defined corresponding voxels across subjects. In this sense, manual ROI delineation is one of the registration methods.</div>
<div>> Because the manual delineation is time consuming, people don't want to do it. Then what we do is to align all images and assume all voxels are registered automatically. This means, if I pick up an arbitrary location (like a single voxel), I can immediately locate the corresponding location (voxel) in each subject by using the same x, y, z coordinates.</div>
<div>> Tractography can also be considered as a registration tool because, for example, we can identify a group of voxels that belong to the corticospinal tract across subjects. Therefore, there is nothing wrong with defining the cst in each subject without image-alignment.</div>
<div>> However, there could be several reasons why you may want to do image alignment (thus voxel-by-voxel registration) first and then additional registration by tractography. First, tractography requires manually (or automatically) defined ROIs for seed and destination. This could be done more reproducibly if all images are aligned. Second, after tracts are defined, you can easily create population-averaged probabilistic maps by simply adding the 3D masking files that define the tract locations. On the other hand, if you are just interested in voxel count (size of the tract) and FA values, image alignment may not be necessary.</div>
<span><font color="#888888">
<div><br></div><div>Susumu</div></font></span></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Aug 16, 2013 at 2:25 AM, <span dir="ltr"><<a href="mailto:wyzyf@mail.ustc.edu.cn" target="_blank">wyzyf@mail.ustc.edu.cn</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
<br>
Hello professor:<br>
<br>
As I understood, fiber tracking analysis with DTI studio should be a group analysis and image registration is<br>
necessary. Am I right?<br>
<br>
I have finished the image registration with DiffeoMap through linear and nonlinear(b0+FA) registration but I don`t<br>
know how to achieve group analysis and the registrated FA doesn`t match the origin vector.<br>
<br>
Thank you very much~!<br>
<br>
Ying Wang<br>
_______________________________________________<br>
mristudio-users mailing list<br>
<a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org" target="_blank">mristudio-users-unsubscribe@mristudio.org</a><br>
</blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
mristudio-users mailing list<br>
<a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org" target="_blank">mristudio-users-unsubscribe@mristudio.org</a><br>
<br></blockquote></div><br></div>
<br>_______________________________________________<br>
mristudio-users mailing list<br>
<a href="mailto:mristudio-users@mristudio.org" target="_blank">mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org" target="_blank">mristudio-users-unsubscribe@mristudio.org</a><br>
<br></blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
mristudio-users mailing list<br>
<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a><br>
<a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>
Unsubscribe, send a blank email to: <a href="mailto:mristudio-users-unsubscribe@mristudio.org">mristudio-users-unsubscribe@mristudio.org</a><br>
<br></blockquote></div><br></div>