[Mrtrix-discussion] help with streamtrack

[Ariel Rokem]

Hi Donald,

First of all, thanks for making mrtrix available! You were right: it wasn't
too painful to get things compiled on fedora. The one comment that I had is
that for some dependencies (gtkglext, in particular) you have to get the
"-devel" version of the library, otherwise the build process throws cryptic
pkg-config errors at you. That might be obvious to some, but got me puzzled
for a bit there. Once I figured that out, though, it went quite smoothly
and I have 0.2.9 running.

Now for a specific question on the "-stop" feature of streamtrack.

Running this command:

streamtrack -seed r_occipital.mif -mask wmMask.mif -include ROI1.mif
-include ROI2.mif SD_STREAM CSD12.mif out.tck -number 1000 -maxnum 1000000

Produces 1000 tracks, as expected, which I can then view in mrview and seem
to be in the right place, except that they go beyond the ROIs. That's where
I thought that "-stop" can come in handy.

Running:

streamtrack -seed r_occipital.mif -mask wmMask.mif -include ROI1.mif
-include ROI2.mif SD_STREAM CSD12.mif out.tck -number 1000 -maxnum 1000000
-stop

On the other hand, produced no tracks at all. Is this just bad luck in the
random choice of seed points within the seed region? I tried it twice, to
convince myself that wasn't it. Is this an expected behavior of
streamtrack? I might be misunderstanding what it's supposed to be doing. I
thought that it would give me roughly the same set of tracks, but clipped
to only the bit of the fiber that is between ROI1 and ROI2.

Thanks again,

Ariel



On Sun, Oct 30, 2011 at 7:14 PM, Donald Tournier <d.tournier at brain.org.au>wrote:

> Hi all,
>
> Nice to see so much discussion going on, keep it up!
>
> Ariel: to answer your question: the -stop option was introduced in 0.2.8.
> Sorry...
>
> Shouldn't be that hard to compile on Fedora though, later versions should
> compile without modification. Let me know if it doesn't...
>
> Cheers,
>
> Donald.
>
>
> On 29 October 2011 10:03, Ariel Rokem <arokem at gmail.com> wrote:
>
>> Hi Thijs,
>>
>> I am following this discussion with some interest:
>>
>> On Fri, Oct 28, 2011 at 2:23 AM, Thijs Dhollander <
>> thijs.dhollander at uzleuven.be> wrote:
>>
>>>
>>>
>>> About your question: what you're looking for is the "*-stop*" option
>>> (with no extra arguments).  If you include this one in your streamtrack
>>> command, all tracks will stop as soon as they enter any of your include
>>> regions: i.e. they will not track beyond your target ROI (but also not
>>> "within", only "up to", I suppose).****
>>>
>>> **
>>>
>>
>> Is this a new feature? I can't seem to find it in 0.2.7, but would rather
>> not have to build from source mrtrix (on fedora...) if that's not necessary
>> in order to get this feature working for me.
>>
>> Thanks,
>>
>> Ariel
>>
>>
>> _______________________________________________
>> 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
>
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