improved readmes

README.md

@@ -4,40 +4,9 @@ and subjects id are randomised.
 
 Each example folder contains 3 subfolders:
  - source, containing the original toy dataset
- - renamed, containing sorted dataset
- - bids, containing bidsified dataset
+ - renamed, empty but will contain dataset dataset
+ - bids,that will contain bidsified dataset
  - resources, containing all nessesairy plugins and files to run the example
+ - README.md file that describe dataset and contain instructions how to each given 
+example 
 
-## 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-Example 1 is based on unpublished study on effet of fatigue on memory performance.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/README.md

@@ -279,6 +279,9 @@ An optional data-processing step can be inserted between preparation and bidsifi
 
 A one-time step of bidsmap creation may be necessary.
 
+> Important: in order to run the examples, an additional package `xlrd` is needed. It allow
+to parce excel files, like the `Apparaiment.xls`
+
 ### <a name="run_prep"></a>Data preparation
 
 In this step, a generic user-defined dataset is organized in a standardized way.