added instructions

README.md

@@ -11,4 +11,33 @@ Each example folder contains 3 subfolders:
 ## Example 1
 Example 1 is based on unpublished study on effet of fatigue on memory performance.
 
+### How to run
+First prepare data from `source` and place it to `renamed`
+```
+python3 $PATH/coinsort.py -r "nii" -t "MRI" example1/source/ example1/renamed/ -p example1/resources/plugins/rename_plugin.py
+```
 
+Next generate an `bidsmap.yaml` configuration file:
+```
+python $PATH/bidsmapper.py example1/renamed/ example1/bids -p example1/resources/plugins/bidsify_plugin.py
+```
+
+The generated file will be placed to `example1/bids/code/bidscoin/bidsmap.yaml`.
+The initial run of `bidsmap` will produce a lot of warnings (> 500), listing
+all nessesary modifications to apply to `bidsmap.yaml` configuration file.
+For conviniance, the warnings and errors will be placed to `example1/bids/code/bidscoin/log/`
+directory.
+
+Apply nessesary modifications and rerun `bidsmapper.py` untill you don't 
+see any warnings and/or errors. You don't need to add `-p example1/resources/plugins/bidsify_plugin.py` after first time, as plugin will be places into configuration file.
+
+Alternatively, you can place already prepeared config file from `example1/resources/map`
+to `example1/bids/code/bidscoin/`
+
+
+Run bidsifier by executing
+```
+python $PATH/bidscoiner.py example1/renamed/ example1/bids
+```
+
+If everything is good, you will retrieve bidsified dataset in `example1/bids/`

example1/resources/map/bidsmap.yaml

@@ -2,7 +2,7 @@ Options:
   version: 2.3.1
   bidsignore: []
 PlugIns:
-  path: test/resources/plugin/bidsify_plugin.py
+  path: example1/resources/plugins/bidsify_plugin.py
   options: {}
 MRI:
   Nifti_SPM12: