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.

3T Diffusion Preprocess Re-run Release

This version is released to use for the re-run of Diffusion Preprocessing on 3T HCP data using the latest version of the eddy binary from FSL.

DO NOT USE THIS VERSION. USE v3.19.0 instead.

7T DeDrift And Resample changes

v3.17.0

Tagging Version v3.17.0

7T ICA FIX bugfix 1

• In fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh: fix use of mask in final location before it is copied there
• In ICAFIX: Revert to using FIX version v1.06 with unreleased melodic binary v3.14a. (a.k.a. FIX version v1.06a)

7T ICA FIX

• Changes necessary to run ICA FIX pipeline on HCP 7T data
• Updated version of FIX tool in use to v1.062 beta
• Included changes to use a scaling formula for all inflated surface generation and add optional extra scaling factor for use on different species (These changes were not included in the version of these scripts used for Structural Preprocessing of 3T data or Supplemental Structural Preprocessing that was done to generate a higher resolution grayordinates space for the 7T data. Therefore, the inflated surfaces that will be released as part of the 7T data release will not include use of the scaling formula for all inflated surfaces.)

BugFix for jacobian usage

PreFreesurfer was failing due to an overlooked call to the topup script, which requires a new argument.

7T Functional Preprocessing

This release contains changes and additions for running the functional preprocessing of 7T HCP data.

It also adds options for a new bias field correction for fMRI, and for mcflirt-based motion correction.

Note, the PreFreeSurfer pipeline has a small error in this release, use version 3.15.1 instead.

BugFix for Random Number Generator Seed

Code to include seed specification in FreeSurferPipeline.sh was accidentally not included in release v3.14.1 as it should have been.

Outlier replacement and random number generator seed specification

This release contains changes to support use of a custom version of the eddy binary that does outlier replacement and also keeps around versions of files without outlier replacement. It also contains changes to support external specification of the seed value supplied to the random number generator used in Structural Preprocessing.

BugFix for ReApplyFix and associated scripts

This release fixes some bugs in Matlab code used by the ReApplyFixPipeline.sh script.

In particular, the fix_3_clean_no_vol.m Matlab code was making a call to the FSL command-line tool fslmaths via the call_fsl() function. This invocation of the fslmaths tool was failing relatively silently. (There was some information in a Matlab log file, but the failure was not being noticed by the calling scripts nor causing any of the calling scripts to report a failure or stop running.) The invocation of the call_fsl() function was replaced with building a command line string and using Matlab's system() function.

Similarly, the functionmotionconfounds.m Matlab code was making a call to the FSL command-line tool fslmaths via a call to the call_fsl() function. This call was also failing relatively silently. The problem was fixed as above by building a command line string and using Matlab's system() function.

The ReApplyFixPipeline is invoked by the DeDriftAndResamplePipeline.sh script. Thus, no earlier version of the HCP Pipelines should be used for running the DeDriftAndResample Pipeline.