How to load FreeSurfer surface files in correct position using Python script

[lassoan (Andras Lasso)]

@mikebind

I don’t understand why the shift would be 0.5 rather than 0.5*voxel dimension

Offset of 0.5 is appropriate if the value is in voxel coordinate system.

@mikebind

For example, the one I am looking at now has voxels which are .97x.97x1mm,

From this data set you won’t learn much. Could you create a data set with FreeSurfer that has much larger voxels than 1mm so that we can see subpixel size misalignments more clearly and make sure we don’t mistake offsets in voxel/physical coordinate systems?

@mikebind

I don’t see how to load a FreeSurfer surface file from a scripted module and specify the reference volume

To make FreeSurfer model loader take into account the reference volume node, specify referenceVolumeID in additional property:

modelNode = slicer.util.loadNodeFromFile('lh.pial', 'FreeSurferModelFile', {'referenceVolumeID': volumeNode.GetID()})

Alternatively, whenever you want to transform a model to RAS coordinate system you can call slicer.modules.freesurferimporter.logic().TransformFreeSurferModelToWorld().