Hi Gabriel,<div><br></div><div>Assuming I understand what you're trying to do, I think you'd be better off splitting your cortical mask into two, one for each hemisphere. You could then do the whole-brain tracking and use all 3 regions (corpus callosum, left cortical & right cortical) as include regions. That should ensure that the tracks you're getting connect both hemispheres through the corpus callosum - which you can't guarantee using a single whole-brain cortical mask. </div>
<div><br></div><div>Your other option is to track using the CC as seed region, specifying -initdir as 1,0,0 (left-right), and your cortical region with -include. That said, I still think you'd be better off splitting your cortical mask into two, to ensure that you're truly getting cortico-cortical connections.</div>
<div><br></div><div>Hope this helps.</div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br><br><div class="gmail_quote">On 11 November 2011 22:32, Gabriel Gonzalez Escamilla <span dir="ltr"><<a href="mailto:ggonesc@upo.es">ggonesc@upo.es</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="font-family:'Times New Roman';font-size:16px"><div><div><div style="font-family:'Times New Roman';font-size:16px">
Dear Thijs,<br><br>Sorry for my insistence, I just want to make sure that you did receive my last mail, because I'm gonna run this on lots of subjects and I would like to know your opinion before doing such amount of work. I must mention that this email is not an exactly copy from the last one, I've add some things.<br>
<br>
First of all thank you again for your answer and time, you are so
helpful, I'd already use the whole brain as seed region as you recommend
me, I use two masks for the -include option and the same brain-mask in
the -mask option see below, as I have no problem with computation time
and space for saving the results, and you are so right I want the most accurate tracking as
possible, so I'd let the number in 10 million, and now I would like to ask
you. <br>
<br>
The thing I'm trying to do is to track all fibers from the corpus
callosum (CC) to the cortex (ctx), for that reason I use the CC and the
ctx as two separated masks to include, I'm using the brain mask as
seeding and mask regions. When I use the -stop option as the CC is so
close to the cortex the tracks generated were just a few (the only ones that were not excluded because they weren't inside the two inclusion areas; and for me they
didn't make much sense, since some of them look like projecting to the pons), so then I did not use the -stop option and the
tracks generated were lots more and of course I have many spurious
tracks (as I see the temporal lobe completely tracked, but a change in the defined options could improve this result, right? I just have to make some probes), I want to be
sure that one of these approaches to get all tracks from CC to ctx is quite good
because I'm going to run this over more than a 100 subjects or if I'm missing something important. I'm using low
thresholds of FA (initcutoff = .2 and cutoff=.1) a -step = .2, and
curvature of 1mm, as recommended for SD_PROB.<br>
<br>
What do you think about it?<br>
<br>
Best Regards,<br>
Gabriel<br>
</div>
</div></div></div><br>-- <br><br><br><br><br>----------------------------<br>PhD. student Gabriel González-Escamilla<br>Laboratory of Functional Neuroscience<br>Department of Physiology, Anatomy, and Cell Biology<br>University Pablo de Olavide<br>
Ctra. de Utrera, Km.1<br>41013 - Seville<br>- Spain -<br><br>Email: <a href="mailto:ggonesc@upo.es" target="_blank">ggonesc@upo.es</a><br><a href="http://www.upo.es/neuroaging/es/" target="_blank">http://www.upo.es/neuroaging/es/</a>
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