Hello, am writing a module which uses FreeSurfer segmentations and surface files. Empirically and based on another discourse post ( Nifti file and freesurfer pial file mismatch in slicer ) I had previously developed a transform to put the pial surface files back in the coordinate system of the segmen…

[image] 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. [image] mikebind: For example, the one I am looking at now has voxels which are .97x.97x1mm, From this data set you …

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

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mikebind (Mike Bindschadler) August 27, 2020, 5:27am 3

Thanks, I’ll try processing a volume with larger and asymmetric voxels, and we can see how it comes out. I should have something to post back tomorrow.

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

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