Create cubic ROI (VOI) and extract data from image file (e.g MRI)?

[lassoan (Andras Lasso)]

@sfglio

I am looking for an option where I can create a mask of the MRI file (like in FSL), create my ROI in this mask and save this mask with the original MRI dimension and including my ROI (like a binary mask). Later it would be great to just extract the MRI data within this cube.

You can import a model of the right shape and size into segmentation node, then export it as labelmap, using the MRI file as reference volume. You can blank out areas outside the segment using Mask Volume effect.

@sfglio

I further want to place multiple ROIs in one mask and calculate distances (distance transformation) and apply a transformation matrix on this mask?

If you want to do this to register segments then you can do this directly using Segment Registration extension. It computes the distance maps, registers them, and returns the resulting transform (linear or deformable). If you want to do this to compute Hausdorff distance or other error statistics then you can use Segment Comparison module.