fsl orient - Shell-Bash

Introduction

fsl orient is a command-line tool in FSL (FMRIB Software Library) that can manipulate the orientation of 3D neuroimaging data. It is often used to reorient the image data to a common standard orientation or to transfer the orientation of one image dataset to another. fsl orient is written in Shell-Bash and can be run in a terminal.

Usage

To use fsl orient, you will first need to install FSL. Once FSL is installed, open a terminal and navigate to the directory containing your 3D neuroimaging data. The basic syntax of fsl orient is as follows:

fslorient -getorient <filename>

This command will return the current orientation of the image data in the file filename. The available options for <filename> include .nii, .nii.gz, .hdr, and .img.

To change the orientation of the image data, you can use the -setsform, -setqform, or -setorientation options followed by a 4x4 matrix. For example:

fslorient -setqform <filename> 1 0 0 0 0 -1 0 0 0 0 1 0 0 0 0 1

This command will set the qform matrix of the image data in filename to a 180-degree rotation around the x-axis.

Conclusion

fsl orient is a powerful tool for manipulating the orientation of 3D neuroimaging data. Its simple command-line interface makes it easy to use in scripts and other automated processes. By using fsl orient, you can ensure that your image data is consistently oriented across subjects, studies, and analysis pipelines.