Hello Jean-Michel,
OpendTect makes a distinction between 2D data (profiles) and 3D data (regularly sampled data), see 
Survey Setup in the training manual. An OpendTect project can be set up for 2D data, for 3D data or for both. All projects must be set up with X,Y coordinates linked to an Inline, Crossline grid. When the project is set up for 3D data, the Inline, Crossline grid is the grid defined by the 3D seismic. OpendTect uses this definition to find seismic inlines and crosslines to display, process and interpret. The 3D seismic data must fall completely inside the Inline, Crossline survey box defined in the survey setup window.
If the project is set up for 2D data only, the Inline, Crossline definition is not that important. 2D lines can stick out of the defined Inline, Crossline survey box. OpendTect finds the information to display, process and interpret from the X,Y information that MUST be present in each trace of the 2D data. The Inline, Crossline definition is only used for gridding operations. 
Coming to your problem. I don't have experience with GPR data but OpendTect does support import of DTZ format data, which is the standard for GPR data. DTZ format must have X,Y coordinates in the headers. You can find the import option under the Survey -> Import -> Seismic Data -> GPR: DTZ format ... menu.
OpendTect can handle crooked 2D lines but I'm not sure what it will do with 2D profiles that fold back on itself. If that creates a problem, you may want to split your profile into 2 or 3 sections: the zig-zag part and the parts that are more or less straight.
I hope this helps.
Best regards,
Paul.
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Paul de Groot
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