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update with fmriprpep 20.XX outputs

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@a3sha2 a3sha2 released this 16 May 00:59
· 286 commits to master since this release
0908955

copy freesurfer from fmirprep/freesufer outputs or option to run fresh freesurfer if wanted::
. struc_process[cxt]=FSF-ACT - FSF for freesurfer
. include struc_freesurferdir[cxt]='path to freesufer dir in design file
. cifti files for cortical thickness and gmd are generated if FSF is included in the process.
. euler number in structural qc
qcanat activated and working!!!
QC for anatomical:

  • euler_number_rh,euler_number_lh - Eurler number if freesurfer is included
  • meanGMD - mean of Grey matter density
  • SignalToNoiseRatio - grey matter signal to noise ratio
  • BackgroundKurtosis - background intensity Kurtosis
  • GreyMatterKurtosis - grey matter intensity Kurtosis
  • EntropyFocusCriterion - entropy focus criterion ( for ghost signals)
  • CorticalContrasts - coritical contrasts between white matter and grey matter signals
  • FGBGEnergyRatio - Foreground-to-background energy ratio
  • ContrastToNoiseRatio - contrast to noise ratio
  • WhiteMatterSkewness - WhiteMatter Skewness
  • BackgroundSkewness - background intensity Kurtosis
    JLF is configured for multi-parallelism option. this is useful for HPC and flywheel. the number of cpu cores can be specified in the design file: jlf_ncpu[cxt]=2 . 2 is default. Parallel configuration is much faster
    the documentation for jlf is activated, struc, gmd, task, qcanat and qc documentations are updated
    fcon design files are updated to remove framewise threshold where it is not needed. Only required for scrubbing.
    task confound can include other confound regressors other than basic 6 motion parameters ( check documentation ). Computing functional connectivity, reho and alff from task is also possible.
    if fmriprep output has freesurfer, ,the residualized bold and res4d (from task) are converted to cifti files as additional outputs.
    task,fcon documentation is updated
    acompcor selection from fmriprep version 20.XX - 5 CSF and 5 WM