Made clearer names for "ds-01/2/3/4" folders; pipeline names in deriv…

…ative folder; markdown file to introduce the Examples branch

examples/BEP001_examples.md

@@ -0,0 +1,21 @@
+# BEP001 examples
+
+This branch of the BEP001 repository contains some practical examples of what a BIDS-compatible qMRI dataset will look like. 
+
+You can find more about the BEP001 addition to the BIDS standard, and the rationale for the additions/changes that it brings to the BIDS format, here: https://github.com/bids-standard/bep001.
+
+ *The datasets in this branch contain empty data files, which might be useful for building simple software tests. 
+ The current branch may eventually be merged with the bids-examples branch of the main bids-standard repo: https://github.com/bids-standard/bids-examples, in which case this disclaimer will be redundant.*
+
+
+## Example 1: MEGRE, multi-echo
+This is a sample dataset from a single MEGRE sequence, which yields multiple images, corresponding to different echo times. This dataset has been used to calculate a quantitative susceptibility map (QSM), as well as a T2* map.
+
+## Example 2: MP2RAGE, single echo
+This is a sample dataset from a standard MP2RAGE sequence, which includes two GRE images acquired after a single inversion pulse. This data have been used to create a T1-map, as well as a T1-weighted image, corrected for B0 and B1-inhomogeneities, which are both part of the example dataset.
+
+## Example 3: MP2RAGE, multi-echo 
+This is a sample dataset from an MP2RAGE sequence with two inversion times, and, for the second inversion time, 4 different echoes.
+
+## Example 4: MultiParameter Mapping (MPM) dataset
+This is a sample dataset from a MultiParameter Mapping (MPM) sequence (as per Weiskopf et al., 2013), which yields multi-echo FLASH scans that are predominantly T1-, PD-, or MT-weighted by changing repetition time and flip angle.

examples/ds-01/dataset_description.json → examples/MEGRE_multiecho/dataset_description.json

@@ -5,5 +5,5 @@
         "Kirstie Whitaker",
         "Gilles de Hollander"
     ],
-    "Description": "This virtual dataset is collected using a single FLASH sequence, which yields multiple images, corresponding to different echo times. This data has been used to calculate a quantitative susceptibility map, as well as a T2* map."
+    "Description": "This virtual dataset is collected using a single MEGRE sequence, which yields multiple images, corresponding to different echo times. This data has been used to calculate a quantitative susceptibility map, as well as a T2* map."
 }