COMP: Added other packages to optionally build

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@176 3db2834d-1276-0410-a171-f2f48b2634cc
COMP: Switch to http from https to avoid certificate errors

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@177 3db2834d-1276-0410-a171-f2f48b2634cc
COMP: Somehow, the git tag that dtiprep requests went away.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@178 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: Added latest ITKv4 rc release fixes.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@179 3db2834d-1276-0410-a171-f2f48b2634cc
COMP:Superbuild issues with svn checkout

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@180 3db2834d-1276-0410-a171-f2f48b2634cc

ENH: Updated to latest versions of ITKv4 and BRAINSTools.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@181 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: 1) DTIPrep creates the output folder via both absolute path (start with /) or relative path (shows only the name of output folder with no symbole /); these paths are used as -f tag in CLP. 2) We added the feature to change the radius and opacity of Sphere of gradient distribution in 3DView, so distribution of multi-b-value gradients is shown. 

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@182 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: Updated versions of software for performance improvments.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@183 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: Removing the bug related to the tag -d for creating default protocol.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@184 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: Adding DTIPrep.xml, in order to support CLP.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@185 3db2834d-1276-0410-a171-f2f48b2634cc
ENH: Adding DTIPrep.xml, in order to support CLP.

git-svn-id: https://www.nitrc.org/svn/dtiprep/trunk@186 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.
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