update paragraph on naming

Author: Remi-Gau

docs/paper/paper.Rmd

@@ -81,12 +81,15 @@ There currently is a python package (pybids, @yarkoni_pybids_2019)
 that "includes virtually any functionality that is likely to be of general use
 when working with BIDS datasets (i.e., that is not specific to one narrow context)".
 
+<!-- Menton ANCPBIDS -->
+
 There are also several MATLAB toolboxes (EEGlab `REF_NEEDED`, CONN toolbox `REF_NEEDED`)
-have some BIDS support, at least to the extend that they can ingest BIDS datasets.
+have some BIDS support, at least to the extend that they can ingest
+raw and/or derivatives BIDS datasets.
 
 <!-- Resting state tooboxes -->
 
-But there is no common library that, independently of the imaging modality,:
+But there is no common library that, independently of the imaging modality:
 - can index and query data and metdata BIDS dataset (whether they are raw or derivatives datasets)
 - helps easily create filenames that follow a BIDS pattern
 - can interact with the BIDS schema
@@ -115,10 +118,11 @@ BIDS-matlab can:
   sessions, runs, modalities, metadata... contained within that dataset (`bids.query`).
 
 BIDS-matlab is able to parse files in a BIDS datasets whether they follow the BIDS schema
-or not, but as long as they only follow BIDS filenaming conventions (like those
-generated by fMRIprep [@esteban_fmriprep_2019]).
+or not, but require that they follow typical BIDS filenaming patterns (like those
+generated by fMRIprep [@esteban_fmriprep_2019] -
+see [next section](#creating-bids-valid-filenames) for more details).
 
-One notable extension was made to the fielname parsing to accomodate filenames
+One notable extension was made to this filename parsing rule to accomodate filenames
 that include a prefix before the standard BIDS filename
 (for example `swuasub-01_task-rest_bold.nii` with the prefix `swua`)
 as prefixing is such a common way to deal with derivatives filenames.
@@ -130,22 +134,23 @@ Most files in a BIDS dataset follow a standard naming convention that can be sum
 ```bash
 datatype/sub-subLabel(_entity-label)*_suffix\.ext
 ```
+<!-- test pseudo regex above and add link and example  -->
 
 As of this writing, the BIDS specfication supports:
 
-- 12 datatypes (for example: `func`, `anat`, `eeg`)
-- 28 different entities (for example: `ses`, `task`, `acq`)
-- 103 suffixes (for example: `bold`, `T1w`, `events`)
+- 12 datatypes (for example: `func`, `anat`, `eeg`...)
+- 28 different entities (for example: `ses`, `task`, `acq`...)
+- 103 suffixes (for example: `bold`, `T1w`, `events`...)
 
 BIDS has a strict set of rules regarding:
 - which suffix and entities are allowed for each datatype,
 - which entities are allowed for raw and derivatives data,
 - which entities are required or optional for each datatype and suffix,
 - which order entities should appear in a filename.
 
-- create BIDS compatible filenames or folder structures for raw or derivatives
-  datasets (`bids.File`, `bids.util.mkdir`,
-  `bids.dataset_description`),
+Creating BIDS valid filenames can therefore become a tedious task.
+BIDS-matlab `bids.File` class can help by relying on the BIDS schema
+to validate filenames upon creation.
 
 ## transformers