Batch resampling

Support
1

Is there a way to use the transform.h5 file from a script to apply the same transform on a batch of volumes? The easiest way would be directly from bash script like:

$ for i in $list;
do Slicer resample \
--transform transform${i}.h5 \
--fixed source${i}.nrrd \
--moving target${i}.nrrd;
done;

A python call would also make it, but I can not find documentation about that…

2

You can do pretty much exactly that in bash using slicer CLI modules as executables using the launcher.

You can also do something similar in python if you would rather.

1 Like
3

Thanks for pointing me to the relevant documentation.

The thing I needed was

Slicer --launch BRAINSResample --help

And the command to run

Slicer --launch BRAINSResample \
--inputVolume source_1.nrrd \
--outputVolume reformated_1.nrrd \
--referenceVolume target_1.nrrd \
--warpTransform transform_1.h5
4

cool - let us know what you find. The log file will show the parameters used when you invoke the cli module via the gui.