[Mrtrix-discussion] Re: Mrtrix-discussion Digest, Vol 13, Issue 2

[Donald Tournier]

Hi Kerstin,

Glad to see there's some healthy discussion going on. I guess you've
pretty much worked everything out already, but just to make life
easier, you might find it useful to create an alias for the mouse
command, rather than creating a whole new duplicate version of it. You
would just need to add a line like this one to your ~/.bashrc file
(assuming you use the BASH shell):

alias streamtrack_mouse='streamtrack -curv X -step Y -minlength Z'

Once you start a new shell, you'll be able to type your command like this:

$ streamtrack_mouse SD_PROB CSD8.mif -seed x,y,z track.tck ....

and the shell will substitute in what you specified as the alias.

And as Wim already pointed out, you can scale the FODs in the overlay
by scaling the FOD in the sidebar using the mouse scroll button, and
then refreshing the main window.

Hope that helps.
Cheers!

Donald.


On Thu, Sep 10, 2009 at 9:19 PM, Kerstin Pannek
<kerstin.pannek at googlemail.com> wrote:
> Hi Wim
>
> thanks for your reply.
> You are right, our gradient encoding was completely wrong - I had to swap z
> and x. I have fixed this now, and I get good tracking results for the
> anterior commissure.
> For streamtrack might just create a second version of it, that uses the
> mouse settings as default. I am mostly working on human data, so I would
> want to keep the original streamtrack defaults somewhere.
> Thanks again for your comments!
>
> Cheers
> Kerstin
>
>
>
> On 10/09/2009, at 7:01 PM, Wim Otte wrote:
>
>> Hi Kerstin,
>>
>> Although you address this question to Donald, I am responding because were
>> are doing csd using mrtrix in rat and mice brains too; and (I could be
>> wrong...) it looks like your orientations are flipped in the dorsal-ventral
>> direction. (As attachment a coronal and transversal screenshot from one of
>> our rat-brains; with blobs).
>>
>> We are able to scale the blobs using the mouse-wheel in the orientation
>> plot window ('side bar'). For fiber tracking in these brains we adjusted the
>> default streamtrack settings.
>>
>> Cheers,
>>
>> Wim Otte
>>
>>
>> On Thu, Sep 10, 2009 at 9:58 AM, <mrtrix-discussion-request at www.nitrc.org>
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-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078