BUG: Shadow variable bug.

An incomplete refactoring of a shadow variable caused
a bug where the values were not being properly maintained.
COMP: Fixed xml parsing error.

Comments must be on one line without line breaks.
COMP: Fixed xml parsing error.

Comments must be on one line without line breaks.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@187 3db2834d-1276-0410-a171-f2f48b2634cc
BUG: Shadow variable bug.

An incomplete refactoring of a shadow variable caused
a bug where the values were not being properly maintained.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@188 3db2834d-1276-0410-a171-f2f48b2634cc
COMP: Optimize for cmake 2.8.9 and fix testing

Some of the testing data resided on a web server
that is no longer in service.  These data sets have
been moved to a more permanent and reliable host
(slicer.kitware.com).

In addition a cmake configuration option for better
performance was added when cmake version 2.8.9 is used.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@189 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: 1) Gradients eddymotioncorrection status bug for multi-scan, 2) the protocol has been changed to include eddymotioncorrection parameters.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@190 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: inconsistent of default protocol by GUI and CL.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@191 3db2834d-1276-0410-a171-f2f48b2634cc
ENH:New features have been included such as brain mask step and dominant direction artifact detector.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@192 3db2834d-1276-0410-a171-f2f48b2634cc
ENH:New features have been included such as brain mask step and dominant direction artifact detector.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@193 3db2834d-1276-0410-a171-f2f48b2634cc
ENH:New features have been included such as brain mask step and dominant direction artifact detector.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@194 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: Update all support packages

Compiler warning in SlicerExecutionModel
NIPYPE incorporation of my patches
SimpleITK upgrade to swig 2.0.8
ITKv4 update with performance improvement
ANTS update with test suite improvements (along
with minor fixes)

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@195 3db2834d-1276-0410-a171-f2f48b2634cc
COMP Remove Qt Moc wrapping of unecessary classes.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@196 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: Removed unnecessary macro.

The MIN, MAX macros often conflict between code sources
and should voided whenever possible.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@197 3db2834d-1276-0410-a171-f2f48b2634cc
COMP: Remove shadow variable warnings.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@198 3db2834d-1276-0410-a171-f2f48b2634cc
COMP: Remove compiler warnings.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@199 3db2834d-1276-0410-a171-f2f48b2634cc
STYLE: Convert CMake-language commands to lower case

Ancient CMake versions required upper-case commands.  Later
command names became case-insensitive.  Now the preferred style
is lower-case.
This also changes all the key words to lower case. The
primary reason for changing key words is that all
documentation for CMakeLists.txt now shows the key words as
lower case. Even the printed “Mastering CMake v5” uses lower
case.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@200 3db2834d-1276-0410-a171-f2f48b2634cc
STYLE: Remove CMake-language block-end command arguments

Ancient versions of CMake required else(), endif(), and similar
block termination commands to have arguments matching the command
starting the block.  This is no longer the preferred style.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@201 3db2834d-1276-0410-a171-f2f48b2634cc
STYLE: Change for development tool compliance

PREMISE:
The  use of the .txx file extension for indicating the file
that is to hold the implementation of a template class is
only adopted by the ITK community and VNL communities (and has
slightly “infected” a few other small components of other projects).
Increasingly tools are being created to help the programmer better
understand and analyze, and provide hints to proper coding options
dynamically in the development environment (color coding, auto-completion).

The obscure .txx file requires special configuration of each development
environment tool to indicate that it is really a c++ header.  For new
developers this is often a difficult and frustrating task.  This is
confirmed by the large amount of documentation for just a few of the
common editors.  Tools that recognize and respect the .hxx extension:
uncrustify, vim, emacs, VisualStudios, clang, SlickEdit,
kwrite, etc....)  None of these tools recognize the .txx extension without
end user customizations.

CONS:
Many files will be changed, and it will not be backwards compatible for
those who accidently included the “.txx” files in their projects.  The .txx
files should not be included in external packages.

BENEFITS:
Implementation files are properly mapped to C++ language type by default
for improved development environment experience.

CONSIDERATIONS:
There is no obvious single correct solution, but in general a common theme
from other guides is that the final extension should be “.hxx” or
some suffix that ends with “.h”.  The extension should be all lower case
letters (to avoid problems on case insensitive file sysetms).

PROPOSAL:
In DTIPrep change all implementation files
that currently have a “.txx” extension to have a “.hxx” extension.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@202 3db2834d-1276-0410-a171-f2f48b2634cc
STYLE: Make all source code conform to similar style.

The source code for DTIPrep has been edited by many developers
and each file had a different indent and format style.  Since
several of the files attempt to be itk compliant, the itk
coding style paradigm was enforced uniformly accross all of
DTIPrep.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@203 3db2834d-1276-0410-a171-f2f48b2634cc
ENH:Adding two features for DWI/DTI QC: brain mask and dominant direction artifact detector,Continue...

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@204 3db2834d-1276-0410-a171-f2f48b2634cc