<div style="font-family: 'Times New Roman'; font-size: 16px;">Now it's donne, I just find the files you sent to Ariel (which I supposed that should be exactly the same that you re-attach to me) and replace the ones I had.<br _moz_dirty="" /><br _moz_dirty="" />Bests,<br _moz_dirty="" />Gabriel<br /><br /><span>El 20/11/11, <b class="name">Robert Smith </b> <r.smith@brain.org.au> escribió:</span><blockquote cite="mid:CAAVKx7Vu6oDGUJust4XLPTh14mdAmwdQyBk-K9Kyzrh-bH1v2w@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">Gabriel<br /><br />I believe the issue you had with the <span style="font-family: courier new,monospace;">-stop</span> option producing very few tracks will be the same issue as was encountered by Ariel earlier this month; the program was terminating each track as soon as it entered <u>any</u> <span style="font-family: courier new,monospace;">-include</span> ROI, and then testing to ensure it had passed through <u>all</u> <span style="font-family: courier new,monospace;">-include</span> ROIs. Those very few tracks you were seeing were probably seeded right at the edge of one of the ROIs such that after one step it was no longer inside that ROI, and could continue tracking to the other include region.<br />
<br />Unfortunately the MRtrix discussion archive seems to have scrubbed my previous message, so I have re-attached the updated code I distributed earlier this month. If you replace the two files in <span style="font-family: courier new,monospace;">(mrtrix_directory)/src/dwi/tractography/tracker/</span> with the two attached files and re-compile MRtrix, the <span style="font-family: courier new,monospace;">-stop</span> option should operate as expected (obviously this won't work if you are using a repository-based version of MRtrix, which only includes the binaries and not the source code).<br />
<br />Best of luck<br />Rob<br clear="all" /><br />--<br /><br />Robert Smith<br />Melbourne Brain Centre<br />245 Burgundy Street<br />Heidelberg VIC 3084<br />Telephone: (+61 3) 9035 7128<br />Fax: (+61 3) 9035 7301<br />Email: r.smith@brain.org.au <r.smith@brain.org.au><br />
<a href="http://www.fni.edu.au" target="_blank">www.florey.edu.au</a> <a href="http://www.brain.org.au" target="_blank">www.brain.org.au</a><br /><span style="font-size: 9pt; font-family: "Times New Roman","serif"; color: red;"></span><br />
<br /><br /><div class="gmail_quote">On Wed, Nov 16, 2011 at 4:13 AM, 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;">thanx for you answer Donald,<br /><br />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 />
<br />Bests,<br />Gabriel<br /><br /><br /><span>El 15/11/11, <b>Donald Tournier </b> <d.tournier@brain.org.au <d.tournier@brain.org.au>> escribió:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div><div class="im">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><div><br /><br /><div class="gmail_quote"><div class="im">On 11 November 2011 22:32, Gabriel Gonzalez Escamilla <span dir="ltr"><ggonesc@upo.es <ggonesc@upo.es> <ggonesc@upo.es <ggonesc@upo.es>>></span> wrote:<br />
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><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 /></div>Email: ggonesc@upo.es <ggonesc@upo.es> <ggonesc@upo.es <ggonesc@upo.es>><div class="im">
<br /><a href="http://www.upo.es/neuroaging/es/" target="_blank">http://www.upo.es/neuroaging/es/</a>
<br />_______________________________________________<br />
Mrtrix-discussion mailing list<br />
</div>Mrtrix-discussion@www.nitrc.org <Mrtrix-discussion@www.nitrc.org> <Mrtrix-discussion@www.nitrc.org <Mrtrix-discussion@www.nitrc.org>><br />
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br />
<br /></blockquote></div><div class="im"><br /><br clear="all" /><div><br /></div>-- <br />Jacques-Donald Tournier (PhD)<br />Brain Research Institute, Melbourne, Australia<br />Tel: <a href="tel:%2B61%20%280%293%209035%207033" target="1" value="+61390357033">+61 (0)3 9035 7033</a><br />
</div></div>
</div></blockquote></div><br />-- <br /><div class="HOEnZb"><div class="h5"><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 <ggonesc@upo.es><br /><a href="http://www.upo.es/neuroaging/es/" target="_blank">http://www.upo.es/neuroaging/es/</a></font>
</div></div><br />_______________________________________________<br />
Mrtrix-discussion mailing list<br />
Mrtrix-discussion@www.nitrc.org <Mrtrix-discussion@www.nitrc.org><br />
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br />
<br /></blockquote></div><br />
</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>