BIDS Manager

Package to collect, organise, manage, and analyse neuroscience data in Brain Imaging Data Structure (BIDS) format.

Version

BIDS Manager version 1.4.3

Compiled version

You can download a compiled version from here.

Features

• Collect data in differents format:
  • DICOM
  • Nifti
  • Micromed (.trc)
  • Brain products (.vhdr)
  • EDF+ (.edf)
  • EEGLAB (.set)
  • 4D neuroimaging
• Organise data in BIDS format
• Offer graphical interface to visualise/manage BIDS dataset
• Run analysis with BIDS Manager-Pipeline

Main Requirements

• Python >= 3.7
• AnyWave, available here: http://meg.univ-amu.fr/wiki/AnyWave
• dicm2nii.exe (is a Windows compiled version of dicm2nii.m https://github.com/xiangruili/dicm2nii) and requires the version 9.5 (R2018b) of the MATLAB Runtime (http://www.mathworks.com/products/compiler/mcr/index.html)

Dependencies

• pydicom
• PyQt5
• bids-validator
• nibabel
• xlrd
• paramiko
• tkcalendar
• pywin32
• pysimplegui
• scipy
• openpyxl

How to debug it

1. Take the following folders from ./app_utils folder and move them to the root folder of the project:
   1. deface_needs
   2. SoftwarePipeline
2. Run the script bids_manager.py to start the app.

Pipelines

You can to do data analysis with softwares defined in SoftwarePipeline. There are two files .json (as templates) for computing ICA and power spectral density with Anywave, but you can add your own software as soon as it works with command line executions.

Authors & Maintainers

• BIDS Manager developper: Nicolas Roehri roehri.nicolas@gmail.com
• BIDS Uploader developper: Samuel Medina samuel.medinavillalon@gmail.com
• BIDS Manager-Pipeline developper: Aude Jegou jegou.aude@gmail.com
• Maintainer: Christian Ferreyra chrisferreyra13@gmail.com
• Maintainer: Maria Fratello maria.fratello97@gmail.com

How to cite

• Roehri, N., Medina-Villalon, S., Jegou, A., Colombet, B., Giusiano, B., Ponz, A., & Bénar, C. G., Transfer, collection and organisation of electrophysiological and imaging data for multicenter studies.

License

This project is licensed under the GPLv3 license.

An example dataset is available here: https://figshare.com/articles/Example_Dataset_for_BIDS_Manager/11687064

BIDS Uploader

Package to transfer data and prepare them for importation in BIDS Dataset. It can be used in local through BIDS Manager or it can be used in sFTP mode to send data to another center.

sFTP Mode

To distribute BIDS uploader to different center, you have to compile it with the good information (host(IP), port, ssh key, protocole name, and secret key). These informations have to be filled in the code generic_uploader\generic_uploader.py at the lines 239-249. Then, you can compile it with the command below:

pyinstaller --onefile --name BIDS_Uploader generic_uploader\\generic_uploader.py

To compile bids_uploader for another version of python (windows 32bits) change your python path in Environment Variable

The executable BIDS_uploader.exe can be distributed to the centers with the following files (stored in "config" folder):

• config\requirements.json (Requirements of the BIDS dataset)
• config\private_ssh_key