[Mrtrix-discussion] RE: Mrtrix-discussion Digest, Vol 33, Issue 9

[Donald Tournier]

Hi Gabriel,

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.

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.

Hope this helps.
Cheers,

Donald.



On 11 November 2011 22:32, Gabriel Gonzalez Escamilla <ggonesc at upo.es>wrote:

> Dear Thijs,
>
> 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.
>
> 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.
>
> 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.
>
> What do you think about it?
>
> Best Regards,
> Gabriel
>
> --
>
>
>
>
> ----------------------------
> PhD. student Gabriel González-Escamilla
> Laboratory of Functional Neuroscience
> Department of Physiology, Anatomy, and Cell Biology
> University Pablo de Olavide
> Ctra. de Utrera, Km.1
> 41013 - Seville
> - Spain -
>
> Email: ggonesc at upo.es
> http://www.upo.es/neuroaging/es/
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>


-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20111115/5a84efaa/attachment.html