Simple script to transform 3D nifti files to fancy gifs! Only works on Mac and Linux.

This package uses the open-source Imagemagick software to convert nifti-files to png-files and subsequently merges these into a gif. Without this software installed on your system, nifti2gif won't work. This package moreover depends on the following Python packages:

• nibabel
• joblib (optional; for parallel processing)

Optionally, to use the reorientation and skullstripping functionality, make sure FSL is installed (and the BET and reorient2std are listed in the PATH).

Unfortunately, no pip-install (through pypi) possible (yet), but you can install it using pip from the Github repo directly:

$ pip install git+https://github.com/lukassnoek/nifti2gif.git@master

Or, alternatively, download the package as a zip-file from Github, unzip, and run:

$ python setup.py install

Use the command-line interface as follows:

$ nifti2gif [-h] -f FILE [-d DIRECTION] [-s SCALE] [-k SKIP] [-t TRIM]
[-r REORIENT] [-b BET] [-F BET_F] [-g GIFNAME] [-D DELAY]
[-l LOOP] [-n N_PROC]

The only mandatory argument is the filename (-f flag), so this is nifti2gif's basic usage:

$ nifti2gif -f my_nifti_file.nii.gz

Optional arguments are:

-h, --help	show this help message and exit
-f FILE, --file FILE
	Filename of nifti to process.
-d DIRECTION, --direction DIRECTION
	Direction (orientation) of gif-movie
-s SCALE, --scale SCALE
	Scale ("size") of gif-image
-k SKIP, --skip SKIP
	How many slices to skip from beginning
-t TRIM, --trim TRIM
	How many slices to trim from the end
-r REORIENT, --reorient REORIENT
	Whether to run reorient2std (FSL)
-b BET, --bet BET
	Whether to run bet (FSL)
-F BET_F, --bet_f BET_F
	What fractional intensity (bet option) to use
-g GIFNAME, --gifname GIFNAME
	How to name the gif-file
-D DELAY, --delay DELAY
	The delay (in ms) of the images in the gif
-l LOOP, --loop LOOP
	How many times to loop the gif
-n N_PROC, --n_proc N_PROC
	How many cpus (processes) to use