segVoxReassign
This repository contains MATLAB tools for remapping large Allen Brain Atlas segmentation IDs (usually uint32 or uint64) to more manageable uint16 ranges.
Overview
When working with Allen Brain Atlas data, the segmentation IDs can be unwieldy due to their large values. This tool provides a streamlined approach to remap these values while maintaining the integrity of the segmentation data.
Key Features
- Converts segmentation IDs from uint32/uint64 to uint16 format
- Preserves hemisphere distinctions in the remapping
- Generates mapping hash tables for cross-reference
- Produces quality control visualizations
Main Function: allen_segid_remap
function newI = allen_segid_remap(segname, outname, outext, is2bg, bgvals, addval)
Parameters:
segname: Filename of input segmentation volumeoutname: Filename of new uint16 valued segmentation volumeoutext: File extension of output volume (.mat, .vtk, .nii)is2bg: Binary flag for whether the original volume has 2 background valuesbgvals: Values assigned as background labelsaddval: Value to add to denote hemisphere split
Outputs:
newI: New uint16 segmented volumeBAP2Allen_segids_hash.csv: Mapping between original and new IDs- Quality control figures
Example Usage
% Example: Remapping Allen segmentation with two background values
allen_segid_remap('allen_seg.vtk', 'allen_seg_remapped', '.nii', 1, [0, 100000], 10000);