Hi Kevin;<br><br>1) What we call, "CST" is actually the mixture of the CST and cortico-pontine-cerebellar pathways.<br>2) once the CST tract leaches pons, the CST branches to the real CST that penetrate the pons toward the spinal cord and the cortico-pontine-cerebellar pathways.<br>
3) The latter pathways outnumber the real CST by far.<br>4) Of course, DTI, which is pixel-by-pixel imaging, can not distingish these two pathways when they bifurcate at the pons.<br>5) Anatomically, the best ROI positoins for the CST would be one at the motor cortex and the other at the medula or spinal cord, which can eliminate all cortico-pontine-cerebellar pathways effectively.<br>
6) However, if you use this combination (similar to what you did: use NOT to remove that latter pathways), the tractography results become unstable because so many exit to the cerebellum (which is anatomically correct) and subtle differences in pixel locations and partial voluming could afect the outcome.<br>
7) That is the reason we reconstructed only up to the cerebral peduncle, avoiding the complex pons area. <br>8) Some more elaborated tractography methods, either deterministic approaches with some kinds of regularization or probabilistic methods may provide more stable results, less affected by a small number of pixels that would wobble due to mixed fibers, but what these provide is mathematically more stable solution, not necessarily anatomically more correct solution. Nonetheless, they could be usefull tools as long as you know the nature of the tool well. <br>
<br>If your finiding, the CST is located too lateral, is a reproducible finding among different subjects, you may want to check your DTI processing pipeline.<br><br>One of the most common mistakes is how oblique angles are handled. GE, Philips (non-overplus), and Siemens (the latest version VB15?) do not require any procedure to incorporate the oblique information, but Philips (overplus) and Siemens (previous version) require recalculation of gradient table based on the oblique angles. If you are using DICOM or Mosaic, this can be easily done by check a box beneath the gradient table window.<br>
<br>Susumu<br><br><br><div class="gmail_quote">On Wed, Jul 1, 2009 at 9:23 AM, Kevin Spitler <span dir="ltr"><<a href="mailto:kevinspitler@ucla.edu">kevinspitler@ucla.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
I am trying to trace the corticospinal tract using DTI Studio and the<br>
tractography algorithm proposed by Wakana et al 2007 NeuroImage.<br>
After making the 2 ROIs at the cerebral peduncle and then at the<br>
precentral gryus, I find the majority of remaining fibers enter the<br>
cerebellum. After removing these with the "NOT" ROIs, I find the<br>
remaining fibers are very lateral in the cerebral peduncle which is<br>
not the typical position of the corticospinal tract. Is there a<br>
mistake I am making or is there another algorithm for ROI placement<br>
that may be better in my situation?<br>
Thank you for your help<br>
<br>
Best,<br>
Kevin<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>
</blockquote></div><br>