Main new features:
- Add the spatial ICA reclean pipeline (#279) with compiled feature generation (#281)
- Better support non-HCP/non-Siemens T1w, T2w, and T2w-FLAIR images (match mean of BC reference with mean of the input T1w/T2w image) with a new abstracted myelin map BC module to generate MyelinMap_BC files (#249) and associated changes in MSMAll.sh (#251), DeDriftAndResample.sh (#252), and other scripts (#259)
- Added correction for Philips (#271) and fix support for GE Healthcare (#285) fieldmap preprocessing
- Refactor MSMSulc.sh into a module, replacing a section of a PreFreesurfer internal script in the pipelines and to allow different MSMSulc to be run after an initial pipeline run (#290)
- Add multi-echo support to fMRI preprocessing
- Add task fMRI level 3 processing script
- Major improvements to the tICA pipeline, including (#284)
Other additions/changes:
- Refactoring of all pipelines to simplify the I/O interface code (#254, #280)
- MR FIX scripts updates and comments to support additional configurations and fewtimepoints icaDim mode for use with legacy data (#241).
- Modification of aff2rigid and ACPCAlignment for adapting to Non-Human Primates or other brains (#245)
- Enable frame range selection for fMRI runs in SingleSubjectConcat.sh and allow MSMAll to be run on partial timeseries (#247)
- Add custom outlier detection functions for tICA feature generation to maintain compatibility with MATLAB runtime r2017b (#263)
- Update conf2hires to remove reinitialization by bbregister for high resolution data in the FreeSurfer pipeline (#265)
- Introduce tICA weighted mode in RSN regression (#278)
- Add a seconds option for diffusion echo spacing to allow for harmonized time units across pipelines (#291)
- Miscellaneous improvements and bugfixes.
Full list of changes from 4.7.0-->4.8.0 here.