diff --git a/README.md b/README.md index ba134d7f7a81d8c4a73a69b0cc3eb6a0f4ac2d52..0bc462978ad5d07d0e343524cb6f96ac39400ccf 100644 --- a/README.md +++ b/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file that describe dataset and contain instructions how to each given +example -## Example 1 -Example 1 is based on unpublished study on effet of fatigue on memory performance.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/` diff --git a/example1/README.md b/example1/README.md index aca22a0c9cdd11f1f7d4aa0741cb7d3887be2c5c..d16fe0d7cecbc5c7bfe26accbc6a6453cc885645 100644 --- a/example1/README.md +++ b/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.