From d68a255d9c6804584b14fb9182a6d4aa008ead96 Mon Sep 17 00:00:00 2001 From: Beliy Nikita <beliy.nikita@uliege.be> Date: Fri, 31 Jan 2020 15:07:30 +0100 Subject: [PATCH] added instructions --- README.md | 29 +++++++++++++++++++++++++++++ example1/resources/map/bidsmap.yaml | 2 +- 2 files changed, 30 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index d101486..ba134d7 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+++ b/README.md @@ -11,4 +11,33 @@ Each example folder contains 3 subfolders: ## Example 1 Example 1 is based on unpublished study on effet of fatigue on memory performance.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 af020c2..a7ebd37 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: -- GitLab