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@coalsont coalsont released this 13 Aug 20:20
· 903 commits to master since this release
v4.0.1
60a0b50

Various bug fixes, minor functionally additions, example script tweaks, and minor across script harmonization, including:

  • Bash command syntax compatibility with standard MacOS installations
  • Fix bug in ReApplyFixPipeline, which affects the volume (NIFTI) data, in which the non-highpass-filtered volume data was being used, rather than the hp-filtered volume data.
  • Make the polynomial detrending option that was added to hcp_fix_multi_run more numerically robust, and limit it to 5th order or less.
  • Adapted RestingStateStats to use a similar approach to the other pipelines for invoking matlab.
  • Created a script (in global/matlab) to compile all matlab code.
  • Modified MSMAll scripts to support use of multi-run FIX-cleaned data.
  • Bug fixes so that calls to topup and flirt work in the context of FSL 6.0+ (necessitated by changes in how FSL 6.0+ treats multi-frame inputs in certain circumstances). [This is not fully resolved, see below, and #118].
  • Revisions to SetUpHCPPipeline.sh to allow some reliance on $PATH environment variable.
  • Some improvements to the logging functions.
  • Add --delete-intermediates flags to FIX and ReApplyFix family of scripts.

Known issues:

  • Input NIFTI files with a TR that does not use units of seconds result in incorrect TR of outputs - please set the TR in units of seconds before processing (#124)
  • FSL 6.0.0 and 6.0.1 changed how they handle reference images when resampling compared to 5.x, and it is likely that not all pipeline scripts take care to use a single-frame file as reference image (#118)
  • Due to a limitation in FIX's argument parsing, hcp_fix cannot currently be run with motion regression disabled (#108)
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