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gpi-neurotools's Introduction

gpi-neurotools

This repository contains wrappers for working with popular neuroimaging tools (e.g. FSL) and reading/writing popular file formats (e.g. NIfTI) in GPI.

BET brain extraction and FAST segmentation using the BET_FAST node on the GPI canvas

Installation

Follow the instructions in this article for installing new node libraries in GPI.

Dependencies

  • GPI Framework version 1.0.0 or newer (must have the BORG)
  • NIBabel - Python libraries for reading and writing common neuroimaging file formats
    • pip install nibabel - make sure you use the pip associated with GPI's Python
  • FSL - FNIRB Software Library

gpi-neurotools's People

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gpi-neurotools's Issues

ReadNiBabel and WriteNiBabel need support for different orientations

There should be options for indicating the orientation of the data before writing, and this should be taken into account when the affine matrix is considered.

The interface should be intuitive, either with several clear options, or a way of specifying each axis separately. Ideally the user should not have to use a Dimensions or Transpose node before writing or after reading the data.

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