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@coalsont coalsont released this Feb 8, 2021

This release will be used for processing of the HCP-Lifespan (Development and Aging) and Connectomes Related to Human Disease projects going forward.

Main new features:

  • Added a Workbench scene for Structural QC (with some automatically generated snapshots) (#201)
  • Added a Workbench scene for fMRI QC (with some automatically generated snapshots) (#203)
  • Added option for distortion correction using Philips fieldmaps (#191, #194)
  • Added option to DiffPreproc (--select-best-b0) to select the "best" (least-distorted) for each phase-encoding direction as input to topup (#158, #198)

Other additions:

  • Added options in DeDriftAndResample to extract a subset of the runs from multi-run FIX into a new concatenated series (#182)
  • Added a single mode of RSNregression, to apply just temporal regression (#170)
  • Added option to OneStepResampling (--wb-resample) for future wb_command -volume-resample resampling of timeseries (to replace slow fslsplit/convertwarp/applywarp/fslmerge code) (#173). Not enabled yet, as not yet supported by public Workbench release.

Bug fixes/changes:

  • Fix incorrect column header names in stats file (MissingGrayordinates.2.txt) that quantifies overlap between subject ROIs and Atlas (f4afdc5 and 64971e3)
  • 91282 template updated to cifti-2 format (e2d5bba)
  • Some minor diffusion bug fixes/enhancements (#192, #193, #199, #202)
  • Catch command errors in DeDriftAndResample (716e9f4). (Need to review error trapping across all scripts at some point...)

Known Issues:

  • Testing revealed that using Octave mode for multi-run ICA-FIX does not always stably converge. Using Octave mode for multi-run ICA-FIX is not advised at this time.
  • 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)
Assets 2

@coalsont coalsont released this Jun 9, 2020

This release is the version used for HCP Development and HCP Aging data ICA-FIX and MSMAll processing.

Added features:

  • Enabling creation of cleaned movement regressors to apply to spatial ICA-FIX (sICA-FIX) cleaned fMRI data. (#164)
  • Extend the checking of the subcortical segmentation (originally #163) to evaluate, per individual subcortical structure and for the brain mask (at both 1x and 2x voxel resolution dilation), the number of voxels missing, those that overlap, and those that fall outside the Atlas (#165).
  • Changes in sICA-FIX to reduce memory usage when applying hp filtering, estimating the dimensionalities of structured and unstructured noise, and computing variance normalization on volume files (#168).
    Note: the biggest memory reduction is with interpreted matlab mode, with a smaller benefit for compiled matlab mode.

Known Issues:

  • There is a bug in the naming of the column headers of the .txt file that quantifies the missingness/overlap of the subcortical segmentation, which was subsequently fixed with f4afdc5 and 64971e3.
  • Testing revealed that using Octave mode for multi-run ICA-FIX does not always stably converge. Using Octave mode for multi-run ICA-FIX is not advised at this time.
  • 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)
Assets 2