--- a
+++ b/demo/mas_demo.sh
@@ -0,0 +1,108 @@
+#!/bin/bash
+
+#########################################
+# Demonstrate the comman usage of the
+# Multi-Atlas Segmentation (MAS) pipeline
+#########################################
+
+
+# Add niftk installation location to system paths: `PATH` and `LD_LIBRARY_PATH`.
+# This will only work if user followed the installation instruction, and installed packages in the recommended location.
+# If you installed the packages in other locations, please change the variable `$HOME` to your own installed locations.
+
+# Option 1: if user installed the default niftk package
+export PATH=${PATH}:"$HOME/niftk-18.5.4/bin"
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}"$HOME/niftk-18.5.4/bin"
+
+# option 2: if use choose to compile the niftyreg/niftyseg from the source code.
+export PATH=${PATH}:"$HOME/nifty_reg/bin"
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}/"$HOME/nifty_reg/lib"
+export PATH=${PATH}:"$HOME/nifty_seg/bin"
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:"$HOME/nifty_seg/lib"
+
+####################################
+######## prepare demo data #########
+####################################
+
+# (Optional) create demo directory within the current folder (preferrably an empty folder)
+mkdir -p ./demo
+cd ./demo
+
+# Download the "in_vivo" atlas from: https://github.com/dancebean/mouse-brain-atlas
+mkdir -p Atlas
+cd Atlas
+svn export https://github.com/dancebean/mouse-brain-atlas/trunk/FVB_NCrl/in_vivo FVB_NCrl_in_vivo
+# only use three atlas for fast processing and demonstration purpose
+cat FVB_NCrl_in_vivo/template_list.cfg | head -n 3 > FVB_NCrl_in_vivo/template_list_demo.cfg
+cd ..
+
+# create input directory, file, and target list
+mkdir -p ./input
+cd ./input
+target_id="A0"
+svn export https://github.com/dancebean/mouse-brain-atlas/trunk/NeAt/in_vivo/template/$target_id.nii.gz
+echo $target_id > targetlist.txt
+cd ..
+
+# create targetlist (only 1 file)
+ls ./input | head -n 1 | cut -d. -f1 > targetlist.txt
+
+# create output directory
+mkdir -p ./output
+
+
+####################################
+######## start demo script #########
+####################################
+
+# Download the main script if not yet done
+svn export --force https://github.com/dancebean/multi-atlas-segmentation/trunk/MASHelperFunctions.sh
+# (Optional) Download the sample parameter configuration file
+svn export --force https://github.com/dancebean/multi-atlas-segmentation/trunk/parameters_samples/parameter_sample.sh
+# You can edit the advanced parameters to fine-tune the algorithm
+
+# source the main script (or use the location of your own copy)
+source ./MASHelperFunctions.sh
+# Alternatively, if you want to mute the listing of all the available functions, use:
+# source ./MASHelperFunctions.sh > /dev/null 2>&1
+
+# define parameters
+atlas_name="FVB_NCrl_in_vivo"
+atlas_dir="Atlas/$atlas_name"
+target_dir="input"
+result_dir="output"
+target_id="A0"
+target_list="input/targetlist.txt"
+atlas_list=$atlas_dir/template_list_demo.cfg
+exe_mode=local
+parameter_cfg=./parameter_sample.sh
+
+dil_voxel=1
+raw_mask_dir=$result_dir/mask
+dilate_mask_dir=$result_dir/mask_dilate_$dil_voxel
+mask_suffix=".mask.$atlas_name"
+
+
+####################################
+#### Demo script ####
+####################################
+
+# 1. ~~~~~ brain extracting/masking ~~~~~~
+mas_masking_batch -T $target_dir -t $target_list -A $atlas_dir -a $atlas_list -r $result_dir -e $exe_mode # -p $parameter_cfg
+
+# 2. ~~~~~ brain mask dilation (not always necessary, check the quickcheck images to decide) ~~~~~
+mas_mask_dilate_batch $target_list $raw_mask_dir $dilate_mask_dir $mask_suffix $dil_voxel $exe_mode  # -p $parameter_cfg
+# generate quickcheck for dilated mask
+mas_quickcheck $target_dir/$target_id $dilate_mask_dir/$target_id$mask_suffix $result_dir/quickcheck/ \
+               $target_id$mask_suffix.d_$dil_voxel # -p $parameter_cfg
+
+# 3. ~~~~~ bias field correction ~~~~~
+# [Skipped] This is an important step before the parcellation. It is skipped in the demo as the images are already "bias-corrected" using the N4 algorithm
+
+# 4. ~~~~~ parcellation ~~~~~
+mas_parcellation_batch -T $target_dir -t $target_list -A $atlas_dir -a $atlas_list -r $result_dir \
+                       -M $dilate_mask_dir -m $mask_suffix -e $exe_mode # -p $parameter_cfg
+
+# # alternatively, if using non-dilated mask:
+# mas_parcellation_batch -T $target_dir -t $target_list -A $atlas_dir -a $atlas_list -r $result_dir \
+#                        -M raw_mask_dir -m $mask_suffix -e local # -p $parameter_cfg