Concurrence

joss_paper/paper.bib

@@ -35,3 +35,32 @@ @article{Li2016
   journal = {Journal of Neuroscience Methods}
 }
 
+@software{BoreDcm2Bids2023,
+  author = {Boré, Arnaud and Guay, Samuel and Bedetti, Christophe and Meisler, Steven and GuenTher, Nick},
+  doi = {10.5281/zenodo.8342572},
+  month = aug,
+  title = {{Dcm2Bids}},
+  url = {https://github.com/UNFmontreal/Dcm2Bids},
+  version = {3.1.0},
+  year = {2023}
+}
+
+@software{heudiconv23,
+  author = {Halchenko, Yaroslav and Goncalves, Mathias and Velasco, Pablo and di Oleggio Castello, Matteo Visconti and Ghosh, Satrajit and Salo, Taylor and Wodder II, John T. and Hanke, Michael and Sadil, Patrick and Christian, Horea and Dae, Michael and Tilley, Steven and Kent, James and T, Isaac and Brett, Matthew and Amlien, Inge and Gorgolewski, Chris and Markiewicz, Chris and Lukas, Darren Christopher and Callenberg, Keith and Kahn, Aksoo Ari and Macdonald, Austin and Poldrack, Benjamin and Melo, Bruno and Braun, Henry and Lee, John and Pellman, John and Michael},
+  doi = {10.5281/zenodo.8364586},
+  month = sep,
+  title = {{nipy/heudiconv}},
+  url = {https://heudiconv.readthedocs.io/en/latest/index.html},
+  version = {1.0.0},
+  year = {2023}
+}
+
+@software{PET2BIDS_2022,
+  author = {Galassi, Anthony and Norgaard, Martin and Thomas, Adam G. and Gonzalez-Escamilla, Gabriel and Svarer, Claus and Rorden, Chris and Matheson, Granville and Knudsen, Gitte and Innis, Robert and Ganz-Benjaminsen, Melanie and Pernet, Cyril},
+  license = {MIT},
+  month = oct,
+  title = {{PET2BIDS}},
+  url = {https://github.com/openneuropet/PET2BIDS},
+  version = {1.0.0},
+  year = {2022}
+}

joss_paper/paper.md

@@ -17,7 +17,7 @@ authors:
   - name: Emeline Pommier
     equal-contrib: false
     affiliation: 2
-  - name: Gregory Hammad
+  - name: Grégory Hammad
     orcid: 0000-0003-1083-3869
     equal-contrib: false
     affiliation: 1
@@ -46,7 +46,23 @@ The Brain Imaging Data Structure (BIDS) [@Gorgolewski2016] was introduced to cha
 
 Prior to the introduction of the BIDS, the main challenge was to adapt the processing scripts to the different (typically inconsistent) dataset structures. With the advent of the BIDS, the main challenge is now to "bidsify" a given dataset, i.e., adapt a dataset to the BIDS. Not only the image files must be renamed according to the standard, but also the associated metadata must contain all expected values, using expected conventions and measurement units.
 
-The challenge increases for datasets acquired prior to the introduction of BIDS, where often mandatory information may not even be present in the original data, or be encoded in a non-common way. This makes it difficult to use generalized tools like, e.g., [dcm2niix](https://github.com/rordenlab/dcm2niix) [@Li2016]. Any new experimental acquisition protocol may introduce new important metadata, which risks to be ignored by generalized tools. Developers will do their best to incorporate the most popular protocols, but the most exotic ones will be probably overlooked. Other tools, like, e.g., [Bidscoin](https://github.com/Donders-Institute/bidscoin) [@Zwiers2022] may rely on conventions used in the laboratory of the developers, and may be difficult to use in laboratories following different conventions.
+The challenge increases for datasets acquired prior to the introduction of BIDS, where often mandatory information may not even be present in the original data, or be encoded in a non-common way.
+Often, organizer tools, for example, 
+[heudiconv](https://heudiconv.readthedocs.io/en/latest/index.html) [@heudiconv23] or
+[dcm2bids](https://unfmontreal.github.io/Dcm2Bids) [@BoreDcm2Bids2023],
+provide access only to a limited subset of source file metadata.
+As a consequence, any additional metadata, introduced by an experimental acquisition protocol,
+will be ignored, or at least will be difficult to retrieve.
+Developers will do their best to incorporate the most popular protocols,
+but the most exotic ones will be probably overlooked.
+Other tools, like, e.g., [Bidscoin](https://github.com/Donders-Institute/bidscoin) [@Zwiers2022]
+may rely on conventions used in the laboratory of the developers,
+and may be difficult to use in laboratories following different conventions.
+
+Multi-modal datasets provide an additional challenge: the organizer tools usually
+focuses only on one modality, for example
+[pet2bids](https://pet2bids.readthedocs.io/en/latest/index.html) [@PET2BIDS_2022]
+would bidsify only PET data, forcing to use additional tools for EEG or MRI data.
 
 The ideal organizer tool must be able to be flexibly adapted to any original data structure and to any reasonable laboratory practices. It must try to retrieve as much necessary metadata as possible, but also allow the user to add additional metadata. It must suggest to follow the current standard but allow deviations from it, e.g., when a given modality is not defined in BIDS.