diff --git a/bids/README.md b/bids/README.md deleted file mode 100644 index 13b4f47..0000000 --- a/bids/README.md +++ /dev/null @@ -1,235 +0,0 @@ -This script exports imaging data from the NeuroSpin archive into the -BIDS format ([Brain Imaging Data Structure](http://bids.neuroimaging.io)). -The BIDS format has been selected because it is simple, easy to share -and supported by lots of software. We are focused on MRI data but other -modalities can be added (diffusion imaging, behavioral, ...). For a full -description, please consult the -[BIDS specifications](http://bids.neuroimaging.io/bids_spec1.0.0.pdf). - -This script import data, but also: -* all files such as README, CHANGES, dataset_descrption.json ... -* deface anatomical data if you need -* use the Bids-validator - -# Dependencies (can simply pip install packages) - - pip install pandas --user - pip install mne --user - pip install mne-bids --user - pip install pydeface --user - -# Installation and usage: -## With the installation of the module -You can install the unicog repository and use `neurospin_to_bids.py` from anywhere. -To install the module, please tape: - - cd - git clone https://github.com/neurospin/unicog.git - python setup.py install --user - -and use as follow: - - neurospin_to_bids.py -h - -## Without the installation of the module -If you don't want install the module, you can just use the `neurospin_to_bids.py` script as a python script. -Simply download the unicog repository: - - cd - git clone https://github.com/neurospin/unicog.git - -and use as follow for instance: - - python /unicog/bids/neurospin_to_bids.py -h - - -# Preparation of data -## Basic importation -**To import data from NeuroSpin, you have to be connected to the NeuroSpin network.** -The information about subjects and data to import are stored into a **exp_info** directory. For instance: - - ./exp_info - ├── participants.tsv - - -See a small example at [https://github.com/neurospin/unicog/tree/master/bids/test_dataset/](https://github.com/neurospin/unicog/tree/master/bids/test_dataset/) - -Also [https://github.com/neurospin/unicog/tree/master/unicogfmri/localizer_pypreprocess/scripts/exp_info](https://github.com/neurospin/unicog/tree/master/unicogfmri/localizer_pypreprocess/scripts/exp_info) - - -## Advanced importation -The importaiton of events are also possible if the *_events.tsv files are correctly set up. -Here is an example: - - ./exp_info - ├── participants.tsv - └── recorded_events - ├── export_events.py - ├── sub-01 - │ └── ses-01 - │ └── func - │ └── sub-01_ses-01_task-loc_events.tsv - └── sub-02 - └── func - └── sub-02_task-loc_events.tsv - -# Importation of data -Now we set all files into **exp_info** directory, you can launch the importation: - - cd - python neurospin_to_bids.py - -* The `/ - [ses-/] - anat/ - sub­-[_ses-]_T1w.nii[.gz] - -Functional: - - sub­-/ - [ses-/] - func/ - sub­-[_ses-]_task-­[_run-­]_bold.nii[.gz] - -As seen by the examples, if you have a session level, a `ses-` -subfolder is added under the `sub­-` folder and it would -then be the one to contain the modality folders (here, `anat` or `func`). -Moreover it should also form part of the file names. - -The run level `run-` is optional if there is only one functional -run for a particular task. - -There are plenty more optional fields to include in the file names depending -on your needs. For more details on that please check directly the -[BIDS specifications](http://bids.neuroimaging.io/bids_spec1.0.0.pdf). - -Fmap: -This script has an implementation of **case 4: Multiple phase encoded directions** of the BIDS specification. - - sub­-/ - [ses-/] - fmap/ - sub­[_ses-][_acq-