Add metadata with "provenance" (version) of fw-heudiconv used

[yarikoptic]

I have tried to find a dataset among openneuro ones which was generated with fw-heudiconv. Either there is none or there is no annotation of any kind by fw-heudiconv that it is a tool which was used:

(git)smaug:/mnt/datasets/datalad/crawl/openneuro[master]git
$> grep -i flywheel */* 2>/dev/null
ds004413/README.md:These files were obtained from Flywheel, defaced and run through fMRIPrep. 
ds004450/README.md:These files were obtained from Flywheel, defaced and run through fMRIPrep. 

$> grep -i fw-heudiconv */* 2>/dev/null

FWIW in heudiconv we since recent nipy/heudiconv#529 we have been adding metadata on heudiconv used:

(git)smaug:/mnt/datasets/datalad/crawl/openneuro[master]git
$> grep -i HeudiconvVer */* 2>/dev/null
ds004274/task-PSAP_bold.json:  "HeudiconvVersion": "0.11.3+d20220512",
ds004331/task-localizer_bold.json:  "HeudiconvVersion": "0.11.3+d20220512",
ds004331/task-main_bold.json:  "HeudiconvVersion": "0.11.3+d20220512",
ds004466/task-rest_bold.json:  "HeudiconvVersion": "0.11.3",
ds004693/task-localizer_bold.json:  "HeudiconvVersion": "0.13.1",
ds004693/task-main_bold.json:  "HeudiconvVersion": "0.13.1",

so we are adding it per each converted subject/session and then task-* files on top level aggregate common metadata fields across all subject/sessions and thus appear on the top level.

It is not a standard BIDS term. Since then the

• [ENH] introduce GeneratedBy to "core" BIDS bids-standard/bids-specification#440
  was merged and released as a part of BIDS 1.9.0 so now we can use GeneratedBy.

Apparently there is already a good number of openneuro datasets which use GeneratedBy

$ for f in ds00*/dataset_description.json ; do grep -q GeneratedBy $f && {echo $f; jq .GeneratedBy $f}; done | tee /tmp/generated-bys
ds003653/dataset_description.json
[ 
  { 
    "Name": "heudiconv/reproin",
    "Version": "0.5.4",
    "Container": {
      "Type": "singularity",
      "Url": "https://github.com/ReproNim/containers/blob/master/images/repronim/repronim-reproin--0.5.4.sing"
    }
  },
  { 
    "Name": "dcm2niix",
    "Version": "v1.0.20190410  (JP2:OpenJPEG) GCC6.3.0"
  }
]
ds003682/dataset_description.json
[ 
  { 
    "Name": "Custom Python scripts",
    "Description": "Custom python scripts"
  }
]
ds003929/dataset_description.json
[ 
  { 
    "Name": "BIDScoin",
    "Version": "3.6.3",
    "CodeURL": "https://github.com/Donders-Institute/bidscoin"
  }
]
ds004161/dataset_description.json
[ 
  { 
    "Name": "BIDScoin",
    "Version": "3.7.2",
    "CodeURL": "https://github.com/Donders-Institute/bidscoin"
  }
]
ds004401/dataset_description.json
[ 
  { 
    "Name": "petsurfer",
    "Version": "freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275"
  }
]
ds004512/dataset_description.json
[ 
  { 
    "Name": "Manual"
  }
]
ds004632/dataset_description.json
[ 
  { 
    "Name": "FSL ; ANTs ",
    "Version": "v3.0.18 ; 2.1.0"
  }
]
ds004654/dataset_description.json
[ 
  { 
    "Name": "MathWorks MATLAB niftiwrite",
    "Description": "Used to convert the raw DICOM data to NIfTI format.",
    "CodeURL": "https://www.mathworks.com/help/images/ref/niftiwrite.html"
  },
  { 
    "Name": "FreeSurfer's MiDeFace",
    "Version": "7.3.2",
    "Description": "A tool for defacing MRI images in a way that is both minimally invasive and achieves goals of privacy",
    "CodeURL": "https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace"
  }
]
ds004697/dataset_description.json
[ 
  { 
    "Name": "dcm2bids",
    "Version": "2.1.6",
    "Description": "Used to convert and organize dicoms into BIDS"
  },
  { 
    "Name": "Manual",
    "Description": "Added 'IntendedFor' and 'TaskName' keys to fmap and func .json files, respectively"
  },
  { 
    "Name": "pydeface",
    "Version": "2.0.2",
    "Description": "Used to de-face MPRage scans"
  }
]
ds004717/dataset_description.json
[ 
  { 
    "Name": "dcm2bids",
    "Version": "3.0.1",
    "Description": "Used to convert and organize dicoms into BIDS"
  },
  { 
    "Name": "pydeface",
    "Version": "2.0.2",
    "Description": "Used to de-face anatomical scans"
  }
]
ds004730/dataset_description.json
[ 
  { 
    "Name": "MathWorks MATLAB niftiwrite",
    "Description": "Used to convert the raw DICOM data to NIfTI format.",
    "CodeURL": "https://www.mathworks.com/help/images/ref/niftiwrite.html"
  },
  { 
    "Name": "FreeSurfer's MiDeFace",
    "Version": "7.3.2",
    "Description": "A tool for defacing MRI images in a way that is both minimally invasive and achieves goals of privacy",
    "CodeURL": "https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace"
  }
]
ds004731/dataset_description.json
[ 
  { 
    "Name": "MathWorks MATLAB niftiwrite",
    "Description": "Used to convert the raw DICOM data to NIfTI format.",
    "CodeURL": "https://www.mathworks.com/help/images/ref/niftiwrite.html"
  },
  { 
    "Name": "FreeSurfer's MiDeFace",
    "Version": "7.3.2",
    "Description": "A tool for defacing MRI images in a way that is both minimally invasive and achieves goals of privacy",
    "CodeURL": "https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace"
  }
]
ds004733/dataset_description.json
[ 
  { 
    "Name": "MathWorks MATLAB niftiwrite",
    "Description": "Used to convert the raw DICOM data to NIfTI format.",
    "CodeURL": "https://www.mathworks.com/help/images/ref/niftiwrite.html"
  },
  { 
    "Name": "FreeSurfer's MiDeFace",
    "Version": "7.3.2",
    "Description": "A tool for defacing MRI images in a way that is both minimally invasive and achieves goals of privacy",
    "CodeURL": "https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace"
  }
]
ds004866/dataset_description.json
[ 
  { 
    "Name": "ezBIDS",
    "Version": "1.0.0",
    "Description": "ezBIDS is a web-based tool for converting neuroimaging datasets to BIDS, requiring neither coding nor knowledge of the BIDS specification",
    "CodeURL": "https://brainlife.io/ezbids/",
    "Container": {
      "Type": "docker",
      "Tag": "brainlife/ezbids-handler"
    }
  }
]
ds004884/dataset_description.json
[ 
  { 
    "Name": "Manual"
  }
]

so apparently some tools already do it out of the box (e.g. bidscoin), and I filed similar issue within heudiconv to make use of GeneratedBy:

• Add/Extend dataset_description.json:GeneratedBy with information about heudiconv/heuristic (if possible)/dcm2niix nipy/heudiconv#727