PERF: Improve performance for restricted deformation feild.
BF: explicitly specify to use bash instead of generic POSIX compliant sh

As reported in http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=690622 some
scripts have "bashisms" -- features which are present only in bash but not in a
limited, but still POSIX compliant shells such as dash (default on many
systems nowadays to speed up boot etc).

Here is a current list from running bashishsms tool

possible bashism in Scripts/ANTSAverage2DAffine.sh line 22 (let ...):
for x in $LL ; do  PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ;  let NFILES=$NFILES+1  ; done
possible bashism in Scripts/ANTSAverage3DAffine.sh line 29 (let ...):
for x in $LL ; do  PARAM1=` awk -v a=$PARAM1 -v b=$x 'BEGIN{print (a + b)}' ` ;  let NFILES=$NFILES+1  ; done
possible bashism in Scripts/guidedregistration.sh line 4 (unsafe echo with backslash):
echo " USAGE \n  sh command.sh  fixed.nii fixedhipp.nii  moving.nii movinghipp.nii outputname  iterations DIM "
possible bashism in Scripts/landmarkmatch.sh line 4 (unsafe echo with backslash):
echo " USAGE \n  sh $0  fixed.nii fixedhipp.nii  moving.nii movinghipp.nii  ITERATIONS LandmarkWeight "
possible bashism in Scripts/landmarkmatch.sh line 28 (let ...):
let DD=MM-NN
possible bashism in Scripts/landmarkmatch.sh line 37 (let ...):
let DD=MM-NN
possible bashism in Scripts/lohmann.sh line 45 (alternative test command ([[ foo ]] should be [ foo ])):
if [[ ! -s ${OUTPUTNAME}repaired.nii.gz ]] ; then
possible bashism in Scripts/lohmann.sh line 51 (alternative test command ([[ foo ]] should be [ foo ])):
if [[ ! -s $WM ]] ; then
possible bashism in Scripts/lohmann.sh line 57 (alternative test command ([[ foo ]] should be [ foo ])):
if [[ ! -s  ${OUT}max.nii.gz ]] ; then
possible bashism in Scripts/weightedaverage.sh line 3 (unsafe echo with backslash):
echo "Usage: \n sh  weightedaverage.sh  \"Faces*tiff\" \n "

although alternative is to fix the scripts, but IMHO it would be better just to
switch to use bash (present everywhere anyways) for the shell interpreter for
those scripts.
WIP: remove boost
This version added the following main functions:

1) can process multi-modality images
2) added a Markov random field smoothing function to the output of sa
3) added the groupwise label fusion method as described in Wang and Yushkevich, Groupwise Segmentation with Joint Label Fusion, MICCAI 2013.
Adding scripts (in CaseStudy) that can replicate the experiments described in the following paper:

Wang and Yushkevich, Multi-Atlas Segmentation with Joint Label Fusion and Corrective Learning - An Open Source Implementation, Frontiers in Neuroinformatics, 2013.
Merge branch 'master' of https://github.com/stnava/ANTs
ENH: Improve command line parsing code.

Invalid command line options should trigger errors with diagnostics
instead of silently (or quietly) proceeding with partial defaults.

Prefer to throw errors on startup rather than give unexpected
results after hours of processing.
COMP: Remove compiler warning about unused variables
STYLE:  Use consistent formatting

In many places, tabs and spaces were both used and it was
quite difficult to read the code.

In source code files with tabs, the uncrustify program was
run to provide consistent formatting.
Merge pull request #62 from stnava/FortifyCommandLineParsingErrors

Fortify command line parsing errors
ENH:  Adding precision option.
COMP:  Need stdio.h for EOF definition.
COMP: compile error with gcc 4.8 w.r.t. itkSetMacro
COMP: Removed redundant typedef causing warning
COMP: get rid of more GCC 4.8.2 warnings
WIP: naming issues ... maybe
WIP: naming issues ... maybe
WIP: naming issues ... maybe
WIP: naming issues ... maybe
WIP: resolve option naming issue