diff --git a/README.md b/README.md index d1014867863ce39f92bef42f3e714f11ead902ed..ba134d7f7a81d8c4a73a69b0cc3eb6a0f4ac2d52 100644 --- a/README.md +++ b/README.md @@ -11,4 +11,33 @@ Each example folder contains 3 subfolders: ## Example 1 Example 1 is based on unpublished study on effet of fatigue on memory performance.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/` diff --git a/example1/resources/map/bidsmap.yaml b/example1/resources/map/bidsmap.yaml index af020c2f6bd31d3899866468f7d2e236d97df319..a7ebd3701cb500effe182606bbe5538f66baaebc 100644 --- a/example1/resources/map/bidsmap.yaml +++ b/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: