[Mrtrix-discussion] help with streamtrack

Tue Nov 8 17:59:10 PST 2011

Thanks Robert!

That does work as expected. I am wondering whether it is possible to define
the seeds for tracking in the deterministic tracking in a more resolved
manner. That is, how can I initiate tracking from every single voxel in an
ROI and then select only those tracks that go another ROI? Essentially, I
want to get exactly the same results and all the possible results in two
different instantiations of the program. Is that possible?

Cheers,

Ariel

On Wed, Nov 2, 2011 at 5:36 PM, Robert Smith <r.smith at brain.org.au> wrote:

> Hi Ariel
>
> The effect you're seeing appears to be a problem in the way the -stopoption is applied.
> Currently, it detects the moment when the track enters *any* of the
> include regions (effectively a Boolean 'OR' operation), and terminates
> tracking.
> The -include option however specifies that a track must enter *all*regions (a Boolean 'AND' operation) in order to be accepted and written to
> the output file.
> So what's happening, is that the tracks are being stopped as soon as they
> enter one region, none of them are succeeding in reaching the other region,
> and you end up with no tracks!
>
> I will confer with Donald regarding exactly how this option should be
> applied, and it will likely change for the next release. In the time being,
> you have a couple of options:
> * Use one ROI as the seed region, and the other as the include region.
> * Try the update I have attached to this message - these two files replace
> the existing ones in (mrtrix_directory)/src/dwi/tractography/tracker/(rename and keep the existing files just in case). You will need to
> re-compile after replacing the files. This will change the handling of the
> -stop option, and should hopefully make it behave a little more sensibly.
> Note however that it will not yield the cropped portion of tracks between
> the two regions as you expected - it will yield the section of track
> between the seed (wherever that happens to be) and the point at which it
> enters whichever include region it traverses last.
>
> Best regards
> Rob
>
> --
>
> Robert Smith
> Melbourne Brain Centre
> 245 Burgundy Street
> Heidelberg VIC 3084
> Telephone: (+61 3) 9035 7128
> Fax: (+61 3) 9035 7301
> Email:  r.smith at brain.org.au
> www.florey.edu.au <http://www.fni.edu.au>        www.brain.org.au
>
>
>
>
> On Wed, Nov 2, 2011 at 6:48 AM, Ariel Rokem <arokem at gmail.com> wrote:
>
>> 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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>>
>
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