Load DSI Studio (*.trk.gz) or TrackVis (*.trk) tracks in Slicer

diffusion

(Jean Christophe Fillion Robin) #1

Does anyone have experience converting and then loading fibertrack generated by these software into 3D Slicer ?

Is there any recommended pathway to export tracts and import them into Slicer ?

We are thinking of these approaches:

  • improve export to vtk (fiberbundle) in software like DSI Studio.
  • add IO support for .trk.gz, .trk

Thanks for your input

References:

Cc: @Johan_Andruejol @fbudin69500


(Isaiah Norton) #2

I have code to load TrackVis-style trk files. It can create Slicer-style vtkPolyData in memory so would be pretty simple to hook it up as another i/o option. It uses C++11 features, but it’s only a few hundred lines so could be modified … unless we’re flipping switch soon! :stuck_out_tongue_winking_eye:

Have never used DSI Studio data though.


(Andras Lasso) #3

@jcfr When do we plan to switch to c++11? I have trouble building Cleaver on Linux and Mac without c++11, too.


Transition to VTK 8.0
#4

I have been generating .trk streamlines in Dipy and would like to export them to 3d Slicer for visualization and overlay onto images. How can .trk files be imported into 3d Slicer? Thanks


(James Cook) #5

Building on the work of @ihnorton, @Johan_Andruejol and @jcfr solved this for us, the github for the code is here.

I managed to compile in windows with vs 2013.

To make it run it needs to be able to find the dll’s from your compiled copy of slicer. I grabbed all the dll files and threw them in the same directory with the exe. That is the wrong solution, but it works.


#6

Perfect will try it out. Thanks!