This is the repository for CNS. The core of CNS is the pipeline for automated segmentation of WMH, UBO Detector. Below is the methodology paper published in Neuroimage:
Jiyang Jiang, Tao Liu, Wanlin Zhu, Rebecca Koncz, Hao Liu, Teresa Lee, Perminder S. Sachdev, Wei Wen (2018). "UBO Detector - A cluster-based, fully automated pipeline for extracting white matter hyperintensities". Neuroimage 174:539-549
Quick start manual can be found at https://cheba.unsw.edu.au/research-groups/neuroimaging/quick-start-manual, or by clicking Manual -> CNS User Manual in CNS GUI.
- Recent FSL versions (at least from 6.0.6.5) changed cluster command. This will lead to errors and the results of number of clusters being all zeros. A work-around is to replace
${FSLDIR}with/path/to/old/FSLin line 47 of/path/to/CNS/WMH_extraction/WMHextraction/WMHextraction_kNNdiscovery_Step3_5_Nol_count.sh, to force using cluster command in older FSL versions. FSL version 6.0.4 was tested.