diff --git a/README.md b/README.md
index 8570bee..ddbe659 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@ Make sure to also check repositories tagged for the following topics:
- [BIDS](https://github.com/topics/bids)
- [BIDS-Apps](https://github.com/topics/bidsapp)
-- [BIDS-Apps](https://github.com/topics/bids-format)
+- [bids-format](https://github.com/topics/bids-format)
## Contents
@@ -105,10 +105,12 @@ For more information check the [BIDS Apps website](https://bids-apps.neuroimagin
[![Docker version](https://img.shields.io/docker/pulls/nipreps/smriprep.svg?style=plastic)](https://hub.docker.com/r/nipreps/smriprep)
- [BIDSonym](https://github.com/PeerHerholz/BIDSonym): a BIDS app for pseudo-anonymization of neuroimaging data
[![Docker version](https://img.shields.io/docker/pulls/peerherholz/bidsonym.svg?style=plastic)](https://hub.docker.com/r/peerherholz/bidsonym)
-- [babs_tests](https://github.com/PennLINC/babs_tests): Tests for BABS
-
[![Docker version](https://img.shields.io/docker/pulls/pennlinc/toy_bids_app.svg?style=plastic)](https://hub.docker.com/r/pennlinc/toy_bids_app)
+- [aslprep](https://github.com/PennLINC/aslprep): Preprocessing of arterial spin labeling data
+
[![Docker version](https://img.shields.io/docker/pulls/pennlinc/aslprep.svg?style=plastic)](https://hub.docker.com/r/pennlinc/aslprep)
- [qsiprep](https://github.com/PennLINC/qsiprep): Preprocessing and reconstruction of diffusion MRI
[![Docker version](https://img.shields.io/docker/pulls/pennbbl/qsiprep.svg?style=plastic)](https://hub.docker.com/r/pennbbl/qsiprep)
+- [xcp_d](https://github.com/PennLINC/xcp_d): Post-processing of fMRIPrep, nibabies, HCP, and DCAN BOLD derivatives for functional connectivity analysis
+
[![Docker version](https://img.shields.io/docker/pulls/pennlinc/xcp_d.svg?style=plastic)](https://hub.docker.com/r/pennlinc/xcp_d)
- [fitlins](https://github.com/poldracklab/fitlins): Fit Linear Models to BIDS Datasets
[![Docker version](https://img.shields.io/docker/pulls/poldracklab/fitlins.svg?style=plastic)](https://hub.docker.com/r/poldracklab/fitlins)
- [multiscalebrainparcellator](https://github.com/sebastientourbier/multiscalebrainparcellator): Multi-Scale Brain Parcellator, part of the Connectome Mapping Toolkit (CMTK), is a BIDS App that implements a full anatomical MRI processing pipeline, from raw T1w data to structural brain parcellation at five different scales.
@@ -133,82 +135,82 @@ Tools for converting data to/from BIDS from other standard or custom formats and
- [Autobids](https://github.com/khanlab/autobids): Automated Dicom to BIDS and pipelines using compute canada. From the Center for Functional and Metabolic Mapping (CFMM) at Western’s Robarts Research Institute.
[![Last commit](https://img.shields.io/github/last-commit/khanlab/autobids?style=plastic)](https://github.com/khanlab/autobids)
-- [BIDScoin](https://bidscoin.readthedocs.io/en/stable/): BIDScoin converts your source-level neuroimaging data to BIDS
+- [BIDScoin](https://bidscoin.readthedocs.io/en/stable/): BIDScoin converts your source-level neuroimaging data to BIDS
[![Last commit](https://img.shields.io/github/last-commit/Donders-Institute/bidscoin?style=plastic)](https://github.com/Donders-Institute/bidscoin)[![PyPI version](https://badge.fury.io/py/bidscoin.svg)](https://pypi.org/project/bidscoin)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
-- [BIDSconvertR](https://bidsconvertr.github.io/): The BIDSconvertR R package provides a user-friendly workflow with graphical user interfaces. It consists of the following steps: (i) convert DICOM data to NIfTI data using dcm2niix (ii) structure this data according to the BIDS specification (iii) provide the papayaWidget viewer for inspecting the images
+- [BIDSconvertR](https://bidsconvertr.github.io/): The BIDSconvertR R package provides a user-friendly workflow with graphical user interfaces. It consists of the following steps: (i) convert DICOM data to NIfTI data using dcm2niix (ii) structure this data according to the BIDS specification (iii) provide the papayaWidget viewer for inspecting the images
[![Last commit](https://img.shields.io/github/last-commit/bidsconvertr/bidsconvertr?style=plastic)](https://github.com/bidsconvertr/bidsconvertr)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
-- [bidsify](https://github.com/NILAB-UvA/bidsify): Tool to convert source MRI datasets to BIDS-compatible datasets.
+- [bidsify](https://github.com/NILAB-UvA/bidsify): Tool to convert source MRI datasets to BIDS-compatible datasets.
[![Last commit](https://img.shields.io/github/last-commit/NILAB-UvA/bidsify?style=plastic)](https://github.com/NILAB-UvA/bidsify)[![PyPI version](https://badge.fury.io/py/bidsify.svg)](https://pypi.org/project/bidsify)[![Docker version](https://img.shields.io/docker/pulls/lukassnoek/bidsify.svg?style=plastic)](https://hub.docker.com/r/lukassnoek/bidsify)
-- [bidskit](https://github.com/jmtyszka/bidskit/blob/master/docs/QuickStart.md): Utility functions for working with DICOM and BIDS neuroimaging data.
+- [bidskit](https://github.com/jmtyszka/bidskit/blob/master/docs/QuickStart.md): Utility functions for working with DICOM and BIDS neuroimaging data.
[![Last commit](https://img.shields.io/github/last-commit/jmtyszka/bidskit?style=plastic)](https://github.com/jmtyszka/bidskit)[![PyPI version](https://badge.fury.io/py/bidskit.svg)](https://pypi.org/project/bidskit)[![Docker version](https://img.shields.io/docker/pulls/jmtyszka/bidskit.svg?style=plastic)](https://hub.docker.com/r/jmtyszka/bidskit)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
-- [BIDSme](https://gitlab.uliege.be/CyclotronResearchCentre/Public/bidstools/bidsme/bidsme_example/-/tree/master/example1):
+- [BIDSme](https://gitlab.uliege.be/CyclotronResearchCentre/Public/bidstools/bidsme/bidsme_example/-/tree/master/example1):
[![Last commit](https://img.shields.io/github/last-commit/nbeliy/bidsme?style=plastic)](https://github.com/nbeliy/bidsme)[![License: GPL-2.0](https://img.shields.io/badge/License-GPLv2-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-2.0)
-- [BMAT](https://github.com/ColinVDB/BMAT):
+- [BMAT](https://github.com/ColinVDB/BMAT):
[![Last commit](https://img.shields.io/github/last-commit/ColinVDB/BMAT?style=plastic)](https://github.com/ColinVDB/BMAT)[![Docker version](https://img.shields.io/docker/pulls/colinvdb/bmat-dcm2niix.svg?style=plastic)](https://hub.docker.com/r/colinvdb/bmat-dcm2niix)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
-- [BrkRaw](https://github.com/BrkRaw/brkraw): For a preclinical Bruker MRI scanner
+- [BrkRaw](https://github.com/BrkRaw/brkraw): For a preclinical Bruker MRI scanner
[![Last commit](https://img.shields.io/github/last-commit/BrkRaw/brkraw?style=plastic)](https://github.com/BrkRaw/brkraw)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
-- [Clinica](https://aramislab.paris.inria.fr/clinica/docs/public/latest/):
+- [Clinica](https://aramislab.paris.inria.fr/clinica/docs/public/latest/):
[![Last commit](https://img.shields.io/github/last-commit/aramis-lab/clinica?style=plastic)](https://github.com/aramis-lab/clinica)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
-- [dac2bids](https://github.com/dangom/dac2bids): Create a BIDS structure for a DICOM folder.
+- [dac2bids](https://github.com/dangom/dac2bids): Create a BIDS structure for a DICOM folder.
[![Last commit](https://img.shields.io/github/last-commit/dangom/dac2bids?style=plastic)](https://github.com/dangom/dac2bids)
-- [Data2Bids](https://github.com/SIMEXP/Data2Bids): Converts MRI files from extension supported by nibabel into NIfTI and convert them to BIDS
+- [Data2Bids](https://github.com/SIMEXP/Data2Bids): Converts MRI files from extension supported by nibabel into NIfTI and convert them to BIDS
[![Last commit](https://img.shields.io/github/last-commit/SIMEXP/Data2Bids?style=plastic)](https://github.com/SIMEXP/Data2Bids)[![PyPI version](https://badge.fury.io/py/data2bids.svg)](https://pypi.org/project/data2bids)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
-- [Dcm2Bids](https://unfmontreal.github.io/Dcm2Bids/): converts DICOM files using dcm2niix into BIDS
+- [Dcm2Bids](https://unfmontreal.github.io/Dcm2Bids/): converts DICOM files using dcm2niix into BIDS
[![Last commit](https://img.shields.io/github/last-commit/cbedetti/Dcm2Bids?style=plastic)](https://github.com/cbedetti/Dcm2Bids)[![PyPI version](https://badge.fury.io/py/Dcm2Bids.svg)](https://pypi.org/project/Dcm2Bids)[![Docker version](https://img.shields.io/docker/pulls/unfmontreal/dcm2bids.svg?style=plastic)](https://hub.docker.com/r/unfmontreal/dcm2bids)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
-- [Explore ASL](https://exploreasl.github.io/Documentation/1.8.0/Tutorials-ASL-BIDS/): Convert DICOM and NIFTI data to the ASL-BIDS format.
+- [Explore ASL](https://exploreasl.github.io/Documentation/1.8.0/Tutorials-ASL-BIDS/): Convert DICOM and NIFTI data to the ASL-BIDS format.
[![Last commit](https://img.shields.io/github/last-commit/ExploreASL/ExploreASL?style=plastic)](https://github.com/ExploreASL/ExploreASL)
-- [HeuDiConv](https://heudiconv.readthedocs.io/): A flexible DICOM converter for organizing brain imaging data into structured directory layouts
+- [HeuDiConv](https://heudiconv.readthedocs.io/): A flexible DICOM converter for organizing brain imaging data into structured directory layouts
[![Last commit](https://img.shields.io/github/last-commit/nipy/heudiconv?style=plastic)](https://github.com/nipy/heudiconv)[![PyPI version](https://badge.fury.io/py/heudiconv.svg)](https://pypi.org/project/heudiconv)[![Docker version](https://img.shields.io/docker/pulls/nipy/heudiconv.svg?style=plastic)](https://hub.docker.com/r/nipy/heudiconv)[![License: Apache 2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg?style=plastic)](https://opensource.org/licenses/Apache-2.0)
- [Horos (Osirix) export plugin](https://github.com/mslw/horos-bids-output): Horos plugin for BIDS output.
[![Last commit](https://img.shields.io/github/last-commit/mslw/horos-bids-output?style=plastic)](https://github.com/mslw/horos-bids-output)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
-- [niix2bids](https://github.com/benoitberanger/niix2bids): Use this package as a command line to organize your Nifti dataset into BIDS.
+- [niix2bids](https://github.com/benoitberanger/niix2bids): Use this package as a command line to organize your Nifti dataset into BIDS.
[![Last commit](https://img.shields.io/github/last-commit/benoitberanger/niix2bids?style=plastic)](https://github.com/benoitberanger/niix2bids)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
- [OpenfMRI2BIDS](https://github.com/bids-standard/openfmri2bids): Convert OpenfMRI dataset to BIDS
[![Last commit](https://img.shields.io/github/last-commit/bids-standard/openfmri2bids?style=plastic)](https://github.com/bids-standard/openfmri2bids)
-- [PET2BIDS](https://github.com/openneuropet/PET2BIDS): Helps you convert your PET data! raw PET scanner files (for example ecat, dicom) and additional side file like excel sheets.
+- [PET2BIDS](https://github.com/openneuropet/PET2BIDS): Helps you convert your PET data! raw PET scanner files (for example ecat, dicom) and additional side file like excel sheets.
[![Last commit](https://img.shields.io/github/last-commit/openneuropet/PET2BIDS?style=plastic)](https://github.com/openneuropet/PET2BIDS)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
-- [ReproIn](https://github.com/ReproNim/reproin): HeuDiConv-based turnkey solution: a setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners.
+- [ReproIn](https://github.com/ReproNim/reproin): HeuDiConv-based turnkey solution: a setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners.
[![Last commit](https://img.shields.io/github/last-commit/ReproNim/reproin?style=plastic)](https://github.com/ReproNim/reproin)[![Docker version](https://img.shields.io/docker/pulls/repronim/reproin.svg?style=plastic)](https://hub.docker.com/r/repronim/reproin)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
-- [SAMRI](https://doi.org/10.3389/fninf.2020.00005): Full stack Small Animal MRI data analysis package, including the `bru2bids` repositing pipeline, which can convert Bruker archives to the BIDS format. From the ETH and University of Zurich, with collaboration from MIT and Dartmouth College.
+- [SAMRI](https://doi.org/10.3389/fninf.2020.00005): Full stack Small Animal MRI data analysis package, including the `bru2bids` repositing pipeline, which can convert Bruker archives to the BIDS format. From the ETH and University of Zurich, with collaboration from MIT and Dartmouth College.
![](https://img.shields.io/badge/shell-black.svg?style=plastic)[![Last commit](https://img.shields.io/github/last-commit/IBT-FMI/SAMRI?style=plastic)](https://github.com/IBT-FMI/SAMRI)
- [XNAT2BIDS](https://github.com/kamillipi/2bids): Simple xnat pipeline to convert DICOM scans to BIDS-compatible output (nii+json).
![](https://img.shields.io/badge/shell-black.svg?style=plastic)[![Last commit](https://img.shields.io/github/last-commit/kamillipi/2bids?style=plastic)](https://github.com/kamillipi/2bids)
### MEEG
-- [BIDSme](https://gitlab.uliege.be/CyclotronResearchCentre/Public/bidstools/bidsme/bidsme_example/-/tree/master/example1):
+- [BIDSme](https://gitlab.uliege.be/CyclotronResearchCentre/Public/bidstools/bidsme/bidsme_example/-/tree/master/example1):
[![Last commit](https://img.shields.io/github/last-commit/nbeliy/bidsme?style=plastic)](https://github.com/nbeliy/bidsme)[![License: GPL-2.0](https://img.shields.io/badge/License-GPLv2-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-2.0)
-- [Biscuit](https://macquarie-meg-research.github.io/Biscuit/): GUI for easy MEG to BIDS conversion
+- [Biscuit](https://macquarie-meg-research.github.io/Biscuit/): GUI for easy MEG to BIDS conversion
[![Last commit](https://img.shields.io/github/last-commit/Macquarie-MEG-Research/Biscuit?style=plastic)](https://github.com/Macquarie-MEG-Research/Biscuit)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
-- [EEG2BIDS](None): A tool for converting raw EEG and iEEG data into the BIDS standard data structure, prepared for LORIS (Longitudinal Online Research and Imaging System).
+- [EEG2BIDS](None): A tool for converting raw EEG and iEEG data into the BIDS standard data structure, prepared for LORIS (Longitudinal Online Research and Imaging System).
![](https://img.shields.io/badge/Javascript-yellow.svg?style=plastic)[![Last commit](https://img.shields.io/github/last-commit/aces/EEG2BIDS?style=plastic)](https://github.com/aces/EEG2BIDS)
-- [EEGLAB](https://eeglab.org/tutorials/04_Import/BIDS.html): See plugins
+- [EEGLAB](https://eeglab.org/tutorials/04_Import/BIDS.html): See plugins
[![Last commit](https://img.shields.io/github/last-commit/sccn/eeglab?style=plastic)](https://github.com/sccn/eeglab)
-- [FieldTrip - data2bids](https://www.fieldtriptoolbox.org/example/bids/):
+- [FieldTrip - data2bids](https://www.fieldtriptoolbox.org/example/bids/):
[![Last commit](https://img.shields.io/github/last-commit/fieldtrip/fieldtrip?style=plastic)](https://github.com/fieldtrip/fieldtrip)[![License: GPL-3.0](https://img.shields.io/badge/License-GPLv3-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-3.0)
-- [MNE-BIDS](https://mne.tools/mne-bids): MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.
+- [MNE-BIDS](https://mne.tools/mne-bids): MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.
[![Last commit](https://img.shields.io/github/last-commit/mne-tools/mne-bids?style=plastic)](https://github.com/mne-tools/mne-bids)[![PyPI version](https://badge.fury.io/py/mne-bids.svg)](https://pypi.org/project/mne-bids)[![License: BSD-3-Clause](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg?style=plastic)](https://opensource.org/licenses/BSD-3-Clause)
-- [sovabids](https://sovabids.readthedocs.io/en/latest/): A Python package for the automatic conversion of EEG datasets to the BIDS standard, with a focus on making the most out of metadata.
+- [sovabids](https://sovabids.readthedocs.io/en/latest/): A Python package for the automatic conversion of EEG datasets to the BIDS standard, with a focus on making the most out of metadata.
[![Last commit](https://img.shields.io/github/last-commit/yjmantilla/sovabids?style=plastic)](https://github.com/yjmantilla/sovabids)
### physiological
-- [BIDScoin](https://bidscoin.readthedocs.io/en/stable/): BIDScoin converts your source-level neuroimaging data to BIDS
+- [BIDScoin](https://bidscoin.readthedocs.io/en/stable/): BIDScoin converts your source-level neuroimaging data to BIDS
[![Last commit](https://img.shields.io/github/last-commit/Donders-Institute/bidscoin?style=plastic)](https://github.com/Donders-Institute/bidscoin)[![PyPI version](https://badge.fury.io/py/bidscoin.svg)](https://pypi.org/project/bidscoin)
-- [bidsphysio](None): Converts physio data (CMRR, AcqKnowledge, Siemens PMU) to BIDS physiological recording
+- [bidsphysio](None): Converts physio data (CMRR, AcqKnowledge, Siemens PMU) to BIDS physiological recording
[![Last commit](https://img.shields.io/github/last-commit/cbinyu/bidsphysio?style=plastic)](https://github.com/cbinyu/bidsphysio)[![PyPI version](https://badge.fury.io/py/bidsphysio.svg)](https://pypi.org/project/bidsphysio/)[![Docker version](https://img.shields.io/docker/pulls/cbinyu/bidsphysio.svg?style=plastic)](https://hub.docker.com/r/cbinyu/bidsphysio/)
-- [phys2bids](https://phys2bids.readthedocs.io/en/latest/): Python3 library to format physiological files in BIDS.
+- [phys2bids](https://phys2bids.readthedocs.io/en/latest/): Python3 library to format physiological files in BIDS.
[![Last commit](https://img.shields.io/github/last-commit/physiopy/phys2bids?style=plastic)](https://github.com/physiopy/phys2bids)[![PyPI version](https://badge.fury.io/py/phys2bids.svg)](https://pypi.org/project/phys2bids)
### others
-- [convert-eprime](https://github.com/tsalo/convert-eprime): Python functions to convert E-Prime files to csvs. Not currently being developed.
+- [convert-eprime](https://github.com/tsalo/convert-eprime): Python functions to convert E-Prime files to csvs. Not currently being developed.
[![Last commit](https://img.shields.io/github/last-commit/tsalo/convert-eprime?style=plastic)](https://github.com/tsalo/convert-eprime)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
- [DCM2NIIx](https://github.com/neurolabusc/dcm2niix): dcm2nii DICOM to NIfTI converter
[![Last commit](https://img.shields.io/github/last-commit/neurolabusc/dcm2niix?style=plastic)](https://github.com/neurolabusc/dcm2niix)
-- [DICM2NII](https://github.com/xiangruili/dicm2nii): dcm2nii DICOM to NIfTI converter
+- [DICM2NII](https://github.com/xiangruili/dicm2nii): dcm2nii DICOM to NIfTI converter
[![Last commit](https://img.shields.io/github/last-commit/xiangruili/dicm2nii?style=plastic)](https://github.com/xiangruili/dicm2nii)
-- [sim2bids](https://github.com/dissagaliyeva/sim2bids): GUI to easily convert simulation results to BIDS format, according to BEP 34 .
+- [sim2bids](https://github.com/dissagaliyeva/sim2bids): GUI to easily convert simulation results to BIDS format, according to BEP 34 .
[![Last commit](https://img.shields.io/github/last-commit/dissagaliyeva/sim2bids?style=plastic)](https://github.com/dissagaliyeva/sim2bids)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
@@ -254,6 +256,7 @@ Ongoing community proposals for extending the BIDS specification or interoperati
- [BEP023](https://bids.neuroimaging.io/bep023): PET Preprocessing derivatives
- [BEP034](https://bids.neuroimaging.io/bep034): Computational modeling
- [BEP035](https://bids.neuroimaging.io/bep035): Modular extensions for individual participant data mega-analyses with non-compliant derivatives
+- [BEP041](https://bids.neuroimaging.io/bep041): Statistical Model Derivatives