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

[Kerstin Pannek]

Good idea!
Thanks

Kerstin


On 11/09/2009, at 1:07 PM, Donald Tournier wrote:

> 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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>>> ><coronal_rat.png>_______________________________________________
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>
>
>
> -- 
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9496 4078