DeDriftAndResample pipeline prepared for v4.0.0 release

Prepared DeDriftAndResample Pipeline for v4.0.0 release

Main Script: DeDriftAndResample/DeDriftAndResamplePipeline.sh

1. Made sure it has a usage function that uses cat <<EOF
   a. Although several of the parameter descriptions are still TBW
2. Have a get_options function that uses global variable names that are similar to the ones that are used in the main function yet clearly recognizable as those set by the get_options function (names start with p_)
3. main function gets its parameters positionally
4. main function uses local variables instead of global variables from the get_options function
5. All communication with the user (informational and error messages) are via calls to log_* functions defined in a shared standard library of bash functions
6. Verification of the necessary environment variables is done "first thing" in the "global" (i.e. non-function) part of the script.
7. The global (non-function) part of the script checks for the user of positional or named parameters on the command line and only uses the get_options function if named parameters are used on the command line. This (along with some of the other changes above) allows invocation of the script using positional parameters on the command line if desired.
8. All references to the (unsupported) use of Octave instead of MATLAB have been removed
9. Checks for environment variable MATLAB_COMPILER_RUNTIME if the MATLAB run mode is compiled MATLAB
10. Defaults to using interpreted MATLAB

Tests run

"Run to completion" tests (not vetted results tests) have been performed using this release with a pipeline setup file configured to use the following tools:

• Customized version of FSL v5.0.9 - used by the ReApplyFixPipeline.sh script which is invoked by the DeDriftAndResamplePipeline.sh script.
  • "newer-than-released" version of bedpostx_gpu
  • "newer-than-released" version of eddy_cuda
  • "newer-than-released" version of melodic
• Connectome Workbench v1.2.3
• MATLAB R2016b - used by ReApplyFixPipeline.sh script which is invoked by the DeDriftAndResamplePipeline.sh script.