Segmentation Documentation And Script Creation

[KKnoernschild]

Goal

Create segmentation script that can read in a nifti image , and a txt Look Up Table file, and then combine and write those as a segmentation file (.seg.nrrd) using slicer and its' built in python package

directory location / current test files

/Shared/johnsonhj/2018Projects/20181112_RecodeLabelMaps/modified_data
BAWHDAdultAtlas_FreeSurferConventionColorLUT_20160524_ModifiedForSlicer.txt
TRIO_TRIO_MR2_dense_compact_seg.nii.gz