tawilkinson / FLIRT-reg

A python wrapper for FLIRT MRI registration

FLIRT Reg

A simple wrapper for FLIRT registration on large datasets in python

Requirements

• Linux (if on Windows use WSL as per the FSL docs)
• FSL
• Python 3
• Numpy
• Nipype

Installation

1. Clone the repo: git clone https://github.com/tawilkinson/flirt-reg.git
2. Change directory: cd flirt-reg
3. Initialise the gpuoptional submodule: git submodule init then git submodule update
4. Install with setuptools: pip install .

Usage

usage: flirt-reg [-h] [-f FILENAME] [-d DIRNAME [DIRNAME ...]] [-n NUM] [-o OUTPUT] [-v] [-r] [-b] [-c COST]

optional arguments:
  -h, --help            show this help message and exit
  -f FILENAME, --filename FILENAME
                        input image filename. Default: searches current directory for .nii.
  -d DIRNAME [DIRNAME ...], --dirname DIRNAME [DIRNAME ...]
                        input directory name(s). Default: searches same directory for as filename for .nii.
  -n NUM, --num NUM     number of images to process. Default: All images in directory.
  -o OUTPUT, --output OUTPUT
                        output filename. Default: out.csv.
  -v, --verbose         prints debugging information. Default: false.
  -r, --radians         output in radians not degrees. Default: false.
  -b, --brain-extract   Turn off brain extraction. Default: false.
  -c COST, --cost COST  Select a cost function from the following list: [mutualinfo,corratio,normcorr,normmi,leastsq,labeldiff,bbr]

• Running: flirt-reg, this will search for any .NII files in the directory you ran the script in and use the first image as a reference
• Running with inputs:
  • flirt-reg -d <input dir>, specifies a directory to search for .NII files
  • flirt-reg -f <input file>, specifies a reference file
  • flirt-reg -f <input_file> -d <input dir> -b, registers all images in input_dir to the reference, input_file, using brain extraction
• Specifying output: flirt-reg -o <output file>, specifies a name for the output file instead of out.csv