ReApplyFix using FSL v5.0.6

ReApplyFixPipeline was changed to work correctly with FSL v5.0.6 for Hand Reclassifications. This was done to be consistent with previous processing of data for Normal Healthy 3T subjects.

ApplyHandReclassification and ReApplyFix

This version is "prereleased" to use for official runs of the ApplyHandReclassification and ReApplyFix pipelines.

This processing is being run in order to support hand reclassification of components for a select few subjects to be included in the HCP_1200 data release.

This is still a BETA version as it still contains beta-test-ready improvements to the MSM-All processing.

Bugfix for Matlab compilation issues

This beta version fixes Matlab compiler issues. Matlab project files (.prj) now include all toolboxes in path.

Beta Test MSMAll Improvements and Fix 7T Resting State Stats

This version includes beta test ready improvements to MSM-All processing.

It also includes a change to the normalise.m Matlab function that fixes an issue that causing Resting State Stats to fail in the rare case that one column in the Movement_Regressors.txt file is all zeros.

7T Resting State Stats

Released for 7T Resting State Stats processing runs

Alpha Testing for 7T Resting State Stats

• Changed internal documentation in RestingStateStats.m
• Do not calculate CIFTI version of the bias field when --bc-mode=NONE in RestingStateStats.sh

7T Diffusion Preprocessing

Released for 7T Diffusion Preprocessing

Alpha Testing for 7T Diffusion Preprocessing - 2

• Removed attempted support for a multi-token value for the --printcom= option in a number of scripts.
• Improved mechanism for retrieving single-token values for many --option=value style options
• Enhanced the FSL version check in run_eddy.sh to identify the GPU-enabled and non-GPU
  -enabled versions of the eddy binary based upon the FSL version in use.
• Removed fallback to using non-GPU-enabled version of eddy binary when use of GPU-enabled version is requested.

Alpha Testing for 7T Diffusion Preprocessing

• Added step to PostEddy phase of Diffusion Preprocessing to copy some eddy log files from where they are generated by the eddy process to where they are desired to be in the packaged data.
• To accomplish this file copying for 3T subject data that has already been processed a separate "patch" pipeline was created, but future runs of 3T Diffusion Preprocessing should use this version so that they do not require a run of the patch pipeline.

3T Diffusion Preprocessing Re-run with fewer hard-coded eddy options

The previous version (v3.18.0) had a number of hard-coded options supplied to the eddy binary. In order not to force all uses of these scripts to use all of those hard-coded options, some of them were removed from the run_eddy.sh script and left to be passed in via multiple uses of the --extra-eddy-arg= parameter.