Interim Changes
Merge branch 'master' of github.com:Washington-University/Pipelines
Pipeline Alpha 2:

PreFreeSurfer:
•	Add gradient distortion correction module
•	Add MNI templates with the correct FOV for FSL
•	Add Mark’s new DO_mprage.sh script.
•	Make pipeline more generalizable to different kinds of data (e.g. data with only one average, data with no field map, data with a field map, data with reversed readout directions)
•	Add Mark’s new field map code and make it a global script instead of a module
•	Eliminate Code for –usesqform situations (which are eliminated with corrected template)
•	Gradient Distortion of Field Map

FreeSurfer:
•	Commit a change related to mris_make_surfaces
•	Don’t normalize T1w before pial surface
•	Re-Optimize pial surface placement based on T2 on a wider variety of data and newest mris_make_surfaces binary
•	Add a sqrt(T1w/T2w) ratio pial surface placement step

PostFreeSurfer:
•	Delete a bunch of unnecessary commands in CreateRibbon.sh
•	Change spec file distinguishers to .c5.spec and .wb.spec
•	Remove “external binary file” path for GIFTI files that are not external binary files
•	Improve native mesh/native volume spec files to include all data needed for evaluating myelin mapping/surface quality
•	Fix tags for native mesh/native volume surfaces
•	Improve all meshes spec files to include T2w image for other QA
•	Set volume palettes where needed
•	Import FreeSurfer label parcellations
•	Convert -metric-roi-mask, -metric-smoothing (dilate) to wb_command
•	Remove caret_command dependency for CreateRibbon.sh that is no longer needed
•	Add approximate FNIRT-based zblip correction for past MB scans

Generic Volume fMRI:
•	Add gradient distortion correction module
•	Gradient distortion correct the field map
•	Make a scout optional (it will be produced if NONE is specified).
•	Add Mark’s new field map code and make it a global script instead of a module
•	Add option for phase up phase down distortion correction (if I can get it to work now, or a placeholder if not)
•	Make sure it works with 1.6mm fMRI (or arbitrary resolution fMRI data)
•	Add gradient warp to one step resample
•	Fix issues with motion regressors not matching Wash U style (move translations in front, angles in degrees)
•	Incorporate AVI’s awk script for detrending motion regressors (as a separate ‘_dt.txt’ file)

Generic Surface fMRI:
•	Fix creation of zeros in brain ordinates
•	Eliminate Code for –usesqform situations
•	Use new wb_command functions from Tim Coalson to greatly speed up some processing steps.
•	Make sure it works with 1.6mm fMRI (or arbitrary resolution fMRI data)
•	Delete a bunch of unnecessary commands in RibbonVolumeToSurfaceMapping.sh
•	Move QA surface data onto 32k mesh for easier viewing

(Past two commits included in these changes)
Add Examples folder containing shells scripts (misnamed .bat for historical reasons) that contain examples of how to call the pipelines.  These are documentation of examples only and are only meant to work on my file system and machines.
Update PreFreeSurfer/scripts/ACPCAlignment.sh
Update PreFreeSurfer/scripts/ACPCAlignment.sh
Update PreFreeSurfer/scripts/AnatomicalAverage.sh
Update PreFreeSurfer/PreFreeSurferPipeline.sh
Typo in CreateMyelinMaps.sh
Merge branch 'master' of github.com:Washington-University/Pipelines
*Fix problem with lightly myelinated cortex being excluded from pial surface (required hacking mris_make_surfaces) and an approximate grey matter normalization for myelin content
*Add faster config file for FNIRT approximate correction of fMRI zblip distortion
Add new FNIRT config for FNIRT-based zblip correction
Update wb_command
PreFreeSurferPipeline batch file changes for NRG
Merge branch 'master' of github.com:Washington-University/Pipelines
Option to resample to a different resolution’s brainordinates
more batch file changes for NRG
Fixes of Mark's robustfov related changes
Merge branch 'master' of github.com:Washington-University/Pipelines
PreFreeSurfer batch and pipeline running