GithubHelp home page GithubHelp logo

alex-lloyd-93 / heudiconv_bids_conversion Goto Github PK

View Code? Open in Web Editor NEW

This project forked from rhulpsychology/heudiconv_bids_conversion

0.0 0.0 0.0 14 KB

Repository having codes written using heudiconv for conversion of dicoms to BIDS

Python 38.87% Shell 61.13%

heudiconv_bids_conversion's Introduction

HeudiConv_BIDS_conversion

Repository having codes written using heudiconv for conversion of dicoms to BIDS

Update Python for using git on the cluster

source /usr/local/apps/psycapps/config/conda_bash_update

Open another new terminal and run the following command templates:

Generate Heuristics

  • Template
bash <code_folder>/call_heudiconv.sh <Dicom_Folder> <Output_Folder> <Subject_list> <Anonymization_script>
  • Example
bash /MRIWork/MRI-Scratch/HeudiConv_BIDS_conversion/code/call_heudiconv.sh /MRIRaw/MRIRaw07/Demo/ /MRIWork/MRI-Scratch/Sample_BIDS_Dataset '202002040947_19800101XXXX' /MRIWork/MRI-Scratch/Create_BIDS_dataset/code/anon_id.py

Generate the dataset

  • Template
bash <code_folder>/call_heudiconv.sh <Dicom_Folder> <Output_Folder> <Subject_list> <Anonymization_script> <heuristic_file>
  • Example
bash /MRIWork/MRI-Scratch/HeudiConv_BIDS_conversion/code/call_heudiconv.sh /MRIRaw/MRIRaw07/Demo/ /MRIWork/MRI-Scratch/Sample_BIDS_Dataset '202002040947_19800101XXXX' /MRIWork/MRI-Scratch/Create_BIDS_dataset/code/anon_id.py /MRIWork/MRI-Scratch/Create_BIDS_dataset/code/heuristic_template.py

heudiconv_bids_conversion's People

Contributors

ayansengupta avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.