working on documentation

docs/source/index.rst

@@ -3,8 +3,36 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to CNS's documentation!
+CHeBA Neuroimaging Software!
 ===============================
+UBO Detector
+------------
+
+UBO Detector is a cluster-based white matter hyperintensity (WMH) extraction pipeline based on k-nearest neighbors (k-NN) algorithm, using T1-weighted and Fluid Attenuation Inversion Recovery (FLAIR) MRI sequences.
+
+System Requirements
+--------------------
+
+UBO Detector has been tested on both CentOS release 6.8 and macOS Sierra with the following software/toolboxes installed:
+
+- SPM12
+- FSL v5.0
+- MATLAB R2016a or above with the following toolboxes installed\:
+
+    - Image Processing Toolbox (ver 9.5 tested)
+    - Statistics and Machine Learning Toolbox (ver 11.0 tested)
+    - Parallel Computing Toolbox (ver 6.9 tested)
+
+Citation
+---------
+
+If you use UBO Detector, please cite:
+
+*Jiang, J., Liu, T., Zhu, W., Koncz, R., Liu, H., Lee, T., Sachdev, P.S., Wen, W. UBO Detector – A cluster-based, fully automated pipeline for extracting white matter hyperintensities. NeuroImage, doi.org/10.1016/j.neuroimage.2018.03.050 (2018).*
+
+If you use TOPMAL, please cite:
+
+*Jiang, J., Paradise, M., Liu, T., Armstrong, N. J., Zhu, W., Kochan, N. A., Brodaty, H., Sachdev, P. S., Wen, W. The association of regional white matter lesions with cognition in a community-based cohort of older individuals, NeuroImage: Clinical 19:14-21, doi.org/10.1016/j.nicl.2018.03.035 (2018).*
 
 .. toctree::
    :hidden:
@@ -13,7 +41,6 @@ Welcome to CNS's documentation!
    :caption: Contents:
 
    install/install
-   code/*
 
 
 Indices and tables