GEMSe Algorithms - 3dct/open_iA GitHub Wiki

In the sampling configuration, GEMSe users can specify an executable to be used for the actual image processing work. This can be an application or a wrapper shell script calling an application or a script.

Arguments are passed to this executable in the following order:

<Executable> <Additional Arguments> <Output Filename> <Modality Input Files> <Parameter Set>

As an example, the command line GEMSe calls, for a segmentation problem with a single modality input file, and an executable with a single, continouus parameter with range 0..1 and no additional arguments, could look like this:

/path/to/executable /output/path/sample0/label.mhd /input/path/modality0.mhd 0.5

The executable is expected to read the input modalities in any format readable by open_iA (typically, the MetaImage format is used), and to write the result in the MetaImage format, with the given filename.