<div style="font-family: 'Times New Roman'; font-size: 16px;">thanx for you answer Donald,<br _moz_dirty="" /><br _moz_dirty="" />Now i just have the doubt about the -stop option, because in my initial trials this option allows only a few tracks to get produced, but when I'd remove this option, lots and lots of tracks were produced, so I'm wondering how good is to use or not this option.<br _moz_dirty="" /><br _moz_dirty="" />Bests,<br _moz_dirty="" />Gabriel<br _moz_dirty="" /><br /><br /><span>El 15/11/11, <b class="name">Donald Tournier </b> <d.tournier@brain.org.au> escribió:</span><blockquote cite="mid:CAPP9hqRMea2MCBTFiSvpfPe3s7_O2cQewuk1rm+HXUksn0Sqag@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">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"><ggonesc@upo.es <ggonesc@upo.es>></span> wrote:<br />
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); 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: ggonesc@upo.es <ggonesc@upo.es><br /><a href="http://www.upo.es/neuroaging/es/" target="_blank">http://www.upo.es/neuroaging/es/</a>
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<br /></blockquote></div><br /><br clear="all" /><div><br /></div>-- <br />Jacques-Donald Tournier (PhD)<br />Brain Research Institute, Melbourne, Australia<br />Tel: +61 (0)3 9035 7033<br />
</div>
</div></blockquote></div><br />-- <br /><font size="3">--------------------------<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: ggonesc@upo.es<br />http://www.upo.es/neuroaging/es/</font>