diff --git a/data/tools/all_converters.yml b/data/tools/all_converters.yml deleted file mode 100644 index fee3a712..00000000 --- a/data/tools/all_converters.yml +++ /dev/null @@ -1,675 +0,0 @@ ---- -# template -# - name: -# url: URL to repo -# data_types: -# - MRI, EEG, MEG, iEEG, events, physio -# expected_input: -# - DICOM, PAR/REC, tsv -# distribution: -# - name: pypi -# url: https://pypi.org/project/??? -# - name: dockerhub -# url: https://hub.docker.com/r/?? -# language: -# - Python, MATLAB -# documentation: URL to documentation -# comment: -# GUI: false - -- group: - name: MRI and PET converters # <--- get rid of the groups and names. Names will be manually entered in the markdown anyway. - members: - - name: bidsify - url: https://github.com/NILAB-UvA/bidsify - data_types: - - MRI - expected_input: - - DICOM - - PAR/REC - language: - - Python - comment: Tool to convert source MRI datasets to BIDS-compatible datasets. - distribution: - - name: pypi - url: https://pypi.org/project/bidsify - - name: dockerhub - url: https://hub.docker.com/r/lukassnoek/bidsify - - - name: bidskit - url: https://github.com/jmtyszka/bidskit - data_types: - - MRI - expected_input: - - DICOM - language: - - Python - comment: Utility functions for working with DICOM and BIDS neuroimaging data. - documentation: https://github.com/jmtyszka/bidskit/blob/master/docs/QuickStart.md - distribution: - - name: pypi - url: https://pypi.org/project/bidskit - - name: dockerhub - url: https://hub.docker.com/r/jmtyszka/bidskit - license: MIT - - - name: BMAT - url: https://github.com/ColinVDB/BMAT - data_types: - - MRI - expected_input: - - DICOM - distribution: - - name: dockerhub - url: https://hub.docker.com/r/colinvdb/bmat-dcm2niix - language: - - Python - GUI: true - license: GPL-3.0 - - - name: Data2Bids - url: https://github.com/SIMEXP/Data2Bids - data_types: - - MRI - expected_input: - - not DICOM - language: - - Python - comment: | - Converts MRI files from extension supported by nibabel into NIfTI and - convert them to BIDS - distribution: - - name: pypi - url: https://pypi.org/project/data2bids - license: MIT - - - name: Dcm2Bids - url: https://github.com/cbedetti/Dcm2Bids - data_types: - - MRI - expected_input: - - DICOM - language: - - Python - comment: converts DICOM files using dcm2niix into BIDS - documentation: https://unfmontreal.github.io/Dcm2Bids/ - distribution: - - name: pypi - url: https://pypi.org/project/Dcm2Bids - - name: dockerhub - url: https://hub.docker.com/r/unfmontreal/dcm2bids - license: GPL-3.0 - - - name: HeuDiConv - url: https://github.com/nipy/heudiconv - data_types: - - MRI - expected_input: - - DICOM - language: - - Python - distribution: - - name: pypi - url: https://pypi.org/project/heudiconv - - name: dockerhub - url: https://hub.docker.com/r/nipy/heudiconv - documentation: https://heudiconv.readthedocs.io/ - comment: | - A flexible DICOM converter for organizing brain imaging data into - structured directory layouts - license: Apache 2.0 - - - name: OpenfMRI2BIDS - url: https://github.com/bids-standard/openfmri2bids - data_types: - - MRI - expected_input: - - openfMRI datasets - language: - - ??? - comment: Convert OpenfMRI dataset to BIDS - - - name: ReproIn - url: https://github.com/ReproNim/reproin - data_types: - - MRI - expected_input: - - DICOM - language: - - Python - comment: 'HeuDiConv-based turnkey solution: a setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners.' - distribution: - - name: dockerhub - url: https://hub.docker.com/r/repronim/reproin - license: MIT - - - name: XNAT2BIDS - url: https://github.com/kamillipi/2bids - data_types: - - MRI - expected_input: - - DICOM - language: - - shell - comment: | - Simple xnat pipeline to convert DICOM scans to BIDS-compatible output - (nii+json). - - - name: Horos (Osirix) export plugin - url: https://github.com/mslw/horos-bids-output - data_types: - - MRI - expected_input: - - ??? - language: - - objective C - comment: Horos plugin for BIDS output. - GUI: yes - license: GPL-3.0 - - - name: BIDScoin - url: https://github.com/Donders-Institute/bidscoin - data_types: - - MRI - - physiological - - PET - expected_input: - - DICOM - - PAR/REC - - physiological - - PET - - Nifti - language: - - Python - distribution: - - name: pypi - url: https://pypi.org/project/bidscoin - documentation: https://bidscoin.readthedocs.io/en/stable/ - comment: | - BIDScoin is a flexible tool to convert (“coin”) source-level (raw) neuroimaging - data sets to BIDS without needing to code anything. It features automatic - data discovery based on header as well as filesystem information, and comes with - a user-friendly GUI to add missing information and tweak the results. BIDScoin - supports multiple source data formats with plugins (e.g. employing dcm2niix, - spec2nii or nibabel) and allows customization of the prior knowledge about your - data (allowing for fully automatic CLI data conversion if you like). - GUI: yes - license: GPL-3.0 - - - name: BIDSme - url: https://github.com/nbeliy/bidsme - data_types: - - MRI - - EEG - expected_input: - - DICOM - - Nifti - - Brain Vision - documentation: https://gitlab.uliege.be/CyclotronResearchCentre/Public/bidstools/bidsme/bidsme_example/-/tree/master/example1 - language: - - Python - comment: - license: GPL-2.0 - - - name: BrkRaw - url: https://github.com/BrkRaw/brkraw - data_types: - - MRI - expected_input: - - Bruker MRI scanner data - language: - - Python - GUI: yes - comment: For a preclinical Bruker MRI scanner - license: GPL-3.0 - - - name: Clinica - url: https://github.com/aramis-lab/clinica - data_types: - - MRI - expected_input: - - ADNI - - AIBL - - NIFD - - OASIS - - OASIS-3 - language: - - Python - comment: - documentation: https://aramislab.paris.inria.fr/clinica/docs/public/latest/ - license: MIT - - - name: niix2bids - url: https://github.com/benoitberanger/niix2bids - data_types: - - MRI - expected_input: - - Nifti converted from DICOM using dcm2niix - language: - - Python - comment: Use this package as a command line to organize your Nifti dataset into BIDS. - license: GPL-3.0 - - - name: dac2bids - url: https://github.com/dangom/dac2bids - data_types: - - MRI - expected_input: - - DICOM - language: - - Python - comment: Create a BIDS structure for a DICOM folder. - - - name: Autobids - url: https://github.com/khanlab/autobids - data_types: - - MRI - expected_input: - - DICOM - language: - - ??? - comment: | - Automated Dicom to BIDS and pipelines using compute canada. From the - Center for Functional and Metabolic Mapping (CFMM) at Western’s Robarts - Research Institute. - - - name: PET2BIDS - url: https://github.com/openneuropet/PET2BIDS - comment: | - Helps you convert your PET data! raw PET scanner files (for example ecat, dicom) - and additional side file like excel sheets. - data_types: - - PET - expected_input: - - DICOM - - ECAT - language: - - MATLAB - - Python - GUI: false - license: MIT - - - name: Explore ASL - url: https://github.com/ExploreASL/ExploreASL - comment: | - Convert DICOM and NIFTI data to the ASL-BIDS format. - data_types: - - MRI - - ASL - expected_input: - - DICOM - - Nifti - documentation: https://exploreasl.github.io/Documentation/1.8.0/Tutorials-ASL-BIDS/ - language: - - MATLAB - - - name: SAMRI - url: https://github.com/IBT-FMI/SAMRI - comment: | - 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. - data_types: - - MRI - expected_input: - - Bruker ParaVision - - NIfTI - language: - - Python - - shell - documentation: https://doi.org/10.3389/fninf.2020.00005 - GUI: false - - - name: BIDSconvertR - url: https://github.com/bidsconvertr/bidsconvertr - comment: | - 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 - data_types: - - MRI - expected_input: - - DICOM - language: - - R - documentation: https://bidsconvertr.github.io/ - GUI: true - license: GPL-3.0 - - - name: ezBIDS - url: https://github.com/brainlife/ezbids - data_types: - - MRI - - ASL - - events - expected_input: - - DICOM - - NIfTI/JSON - - events (tsv, csv, txt, out, xlsx) - language: - - Vue - - TypeScript - - Javascript - - Python - - shell - documentation: https://brainlife.io/docs/using_ezBIDS/ - comment: | - A web-based BIDS conversion tool with four unique features: - (1) No installation or programming requirements. - (2) Handling of both imaging and task events data and metadata. - (3) Semi-automated inference and guidance for adherence to BIDS. - (4) Multiple data management options, including download BIDS data - to local system, or transfer to OpenNeuro.org or to brainlife.io. - GUI: true - license: MIT - - - name: mercure-dcm2bids - url: https://github.com/mercure-imaging/mercure-dcm2bids - data_types: - - MRI - expected_input: - - DICOM - language: - - Python - documentation: https://github.com/mercure-imaging/mercure-dcm2bids - comment: | - A containerized app that can be used to perform BIDS conversion of - DICOM studies sent directly to mercure from a scanner or PACS. mercure - is an open-source DICOM orchestration platform that can integrate - containerized apps into clinical workflows. It has a graphical user - interface making it easy to setup and manage BIDS configurations for - multiple protocols. The Dcm2Bids tool is used for conversion. - distribution: - - name: dockerhub - url: https://hub.docker.com/r/mercureimaging/mercure-dcm2bids - GUI: true - license: GPL-3.0 - - -- group: - name: EEG, MEG, iEEG converters - members: - - name: BIDSme - url: https://github.com/nbeliy/bidsme - data_types: - - MRI - - EEG - expected_input: - - DICOM - - Nifti - - Brain Vision - language: - - Python - documentation: https://gitlab.uliege.be/CyclotronResearchCentre/Public/bidstools/bidsme/bidsme_example/-/tree/master/example1 - comment: - license: GPL-2.0 - - - name: MNE-BIDS - url: https://github.com/mne-tools/mne-bids - data_types: - - MEG - - EEG - - iEEG - - NIRS - expected_input: - - raw MEG for BIDS conversion - - raw EEG for BIDS conversion - - raw iEEG for BIDS conversion - - raw NIRS for BIDS conversion - - BIDS dataset for reading - language: - - Python - documentation: https://mne.tools/mne-bids - distribution: - - name: pypi - url: https://pypi.org/project/mne-bids - - name: conda-forge - url: https://anaconda.org/conda-forge/mne-bids/ - comment: MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python. - GUI: false - license: BSD-3-Clause - - - name: EEGLAB - url: https://github.com/sccn/eeglab - data_types: - - MEG - - EEG - expected_input: - - EDF - - BDF - - Brain Vision Exchange Format - - EEGLAB .set files - language: - - MATLAB - documentation: https://eeglab.org/tutorials/04_Import/BIDS.html - comment: See plugins - - - name: FieldTrip - data2bids - url: https://github.com/fieldtrip/fieldtrip - data_types: - - EEG - - MEG - - iEEG - - behavioral - - MRI (anat and func) - expected_input: - - any EEG or MEG file format - - NBS Presentation logfiles - - DICOM - - nifti - language: - - MATLAB - documentation: https://www.fieldtriptoolbox.org/example/bids/ - license: GPL-3.0 - - - name: Biscuit - url: https://github.com/Macquarie-MEG-Research/Biscuit - data_types: - - MEG - expected_input: - - ??? - language: - - Python - documentation: https://macquarie-meg-research.github.io/Biscuit/ - comment: GUI for easy MEG to BIDS conversion - GUI: true - license: MIT - - - name: sovabids - url: https://github.com/yjmantilla/sovabids - data_types: - - EEG - expected_input: - - ??? - language: - - Python - documentation: https://sovabids.readthedocs.io/en/latest/ - comment: A Python package for the automatic conversion of EEG datasets to the BIDS standard, with a focus on making the most out of metadata. - - - name: EEG2BIDS - url: https://github.com/aces/EEG2BIDS - data_types: - - EEG - expected_input: - - ??? - language: - - Javascript - - Python - documentation: - comment: A tool for converting raw EEG and iEEG data into the BIDS standard data structure, prepared for LORIS (Longitudinal Online Research and - Imaging System). - - -- group: - name: Physiological data converters - comment: - members: - - name: phys2bids - url: https://github.com/physiopy/phys2bids - data_types: - - phsyiological - expected_input: - - Acqknowledge - - Labchart - - GE physiological files - language: - - Python - distribution: - - name: pypi - url: https://pypi.org/project/phys2bids - documentation: https://phys2bids.readthedocs.io/en/latest/ - comment: Python3 library to format physiological files in BIDS. - license: Apache-2.0 - - - name: bidsphysio - url: https://github.com/cbinyu/bidsphysio - data_types: - - physiological - expected_input: - - CMRR - - AcqKnowledge - - Siemens PMU - distribution: - - name: pypi - url: https://pypi.org/project/bidsphysio/ - - name: dockerhub - url: https://hub.docker.com/r/cbinyu/bidsphysio/ - language: - - Python - documentation: - comment: Converts physio data to BIDS physiological recording - GUI: false - - -- group: - name: "'From BIDS' converters" - comment: Converters that take a BIDS dataset as input to convert it into something else. Not mentioned here are the many software that can import a - BIDS data as data structure they are more familiar with. - members: - - name: BIDS2ISATab - url: https://github.com/bids-standard/BIDS2ISATab - data_types: - - From BIDS - expected_input: - - BIDS - language: - - Python - comment: Extract ISA-Tab compatible metadata from BIDS - license: Apache-2.0 - - - name: BIDSto3col - url: https://github.com/bids-standard/bidsutils/tree/master/BIDSto3col - data_types: - - From BIDS - - TSV - expected_input: - - BIDS - language: - - shell - - Python - comment: Reads BidsTSV and then creates 3 column event files, one per event type if a "trial_type" column is found. - - - name: BIDS2NDA - url: https://github.com/bids-standard/BIDS2NDA - data_types: - - From BIDS - expected_input: - - BIDS - language: - - Python - comment: Extract NIHM Data Archive compatible metadata from BIDS - license: Apache-2.0 - - - name: bids2xar - for XNAT import - url: https://github.com/lwallace23/bids2xar - data_types: - - From BIDS - - MRI # not sure - expected_input: - - BIDS - language: - - Python - comment: Convert BIDS data set into XNAT XAR bundles - - - name: BIDS2NIDM - url: https://github.com/incf-nidash/PyNIDM/blob/master/nidm/experiment/tools/nidm2bids.py - data_types: - - From BIDS - expected_input: - - BIDS - language: - - Python - comment: | - This program will convert a NIDM-Experiment RDF document to a BIDS - dataset. - - - name: AFNI BIDS-tools - url: https://github.com/nih-fmrif/BIDS-tools - data_types: - - From BIDS - - MRI - expected_input: - - BIDS # not sure about that one - language: - - shell - - Python - comment: ARCHIVED - Scripts, tools, and documents on creating, parsing, and working with BIDS-structured data sets. - - -- group: - name: Miscellaneous - comment: Not exactly BIDS converters but are common tools that can used by other BIDS converters. - members: - - name: convert-eprime - url: https://github.com/tsalo/convert-eprime - data_types: - - other converters - - behavioral - expected_input: - - E-Prime log files - language: - - Python - comment: Python functions to convert E-Prime files to CSVs. Not currently being developed. - license: MIT - - - name: DCM2NIIx - url: https://github.com/neurolabusc/dcm2niix - data_types: - - other converters - - DICOM - - PAR/REC - expected_input: - - ??? - language: - - C++ (compiled versions available from NITRC) - comment: dcm2nii DICOM to NIfTI converter - - - name: DICM2NII - url: https://github.com/xiangruili/dicm2nii - data_types: - - other converters - - DICOM - expected_input: - - DICOM - language: - - MATLAB - comment: dcm2nii DICOM to NIfTI converter - license: BSD-2 - - - name: sim2bids - url: https://github.com/dissagaliyeva/sim2bids - data_types: - - computational model - expected_input: - - CSV/TSV/DAT/Numpy - - arrays/HDF5 - - zip folders - - code files in MATLAB/Python/R - language: - - Python - comment: GUI to easily convert simulation results to BIDS format, according to BEP - 34 . - license: MIT diff --git a/data/tools/converters.yml b/data/tools/converters.yml index 100d1a66..362bf3f5 100644 --- a/data/tools/converters.yml +++ b/data/tools/converters.yml @@ -625,30 +625,6 @@ comment: Python functions to convert E-Prime files to CSVs. Not currently being developed. license: MIT - - name: DCM2NIIx - url: https://github.com/neurolabusc/dcm2niix - data_types: - - MISC - - DICOM - - PAR/REC - expected_input: - - ??? - language: - - C++ (compiled versions available from NITRC) - comment: dcm2nii DICOM to NIfTI converter - - - name: DICM2NII - url: https://github.com/xiangruili/dicm2nii - data_types: - - MISC - - DICOM - expected_input: - - DICOM - language: - - MATLAB - comment: dcm2nii DICOM to NIfTI converter - license: BSD-2 - - name: sim2bids url: https://github.com/dissagaliyeva/sim2bids data_types: