flirt_params

Available Keys for the flirt_params in the flirt control JSON file. Input and output files do not need specified here.

Key Name	Required?	Data Type	Description
args	OPTIONAL	string	Additional parameters to the command
angle_rep	OPTIONAL	string	representation of rotation angles: quaternion, euler
apply_isoxfm	OPTIONAL	float	as applyxfm but forces isotropic resampling (NOT SUPPORTED)
apply_xfm	OPTIONAL	boolean	apply transformation supplied by in_matrix_file (NOT SUPPORTED)
bbrslope	OPTIONAL	float	value of bbrslope
bbrtype	OPTIONAL	string	type of bbr cost function: signed [default], global_abs, local_abs
bgvalue	OPTIONAL	float	use specified background value for points outside FOV
bins	OPTIONAL	integer	number of histogram bins
coarse_search	OPTIONAL	integer	coarse search delta angle
cost	OPTIONAL	string	cost function: mutualinfo, corratio, normcorr, normmi, leastsq, labeldiff, bbr
cost_func	OPTIONAL	string	cost function: mutualinfo, corratio, normcorr, normmi, leastsq, labeldiff, bbr
datatype	OPTIONAL	string	force output data type: char, short, int, float, double
display_init	OPTIONAL	boolean	display initial matrix
dof	OPTIONAL	integer	number of transform degrees of freedom
echospacing	OPTIONAL	float	value of EPI echo spacing - units of seconds
environ	OPTIONAL	dictionary	environment variables
fieldmap	OPTIONAL	file name	reference image
fieldmapmask	OPTIONAL	file name	mask for fieldmap image
fine_search	OPTIONAL	integer	fine search delta angle
force_scaling	OPTIONAL	boolean	force rescaling even for low-res images
ignore_exception	OPTIONAL	boolean	print an error message instead of throwing an exception in case that interface fails to run
in_matrix_file	OPTIONAL	file name	input 4x4 affine matrix
in_weight	OPTIONAL	existing file name	file for input weighting volume
interp	OPTIONAL	string	final interpolation method used in reslicing: trilinear, nearestneighbor, sinc, spline
min_sampling	OPTIONAL	float	set minimum voxel dimension for sampling
no_clamp	OPTIONAL	boolean	do not use intensity clamping
no_resample	OPTIONAL	boolean	do not change input sampling
no_resample_blur	OPTIONAL	boolean	do not use blurring on downsampling
no_search	OPTIONAL	boolean	set all angular searches to ranges 0 to 0
out_file	OPTIONAL	file name	registered output file
out_log	OPTIONAL	file name	output log
out_matrix_file	OPTIONAL	file name	output affine matrix in 4x4 asciii format
output_type	OPTIONAL	string	FSL output type: NIFTI_PAIR, NIFTI_PAIR_GZ, NIFTI_GZ, NIFTI
padding_size	OPTIONAL	integer	for applyxfm: interpolates outside image by size
pedir	OPTIONAL	integer	phase encode direction of EPI - 1,2,3=x,y,z & -1,-2,-3=x,-y,-z
ref_weight	OPTIONAL	existing file name	file for reference weighting volume
rigid2D	OPTIONAL	boolean	use 2D rigid body mode - ignores dof
save_log	OPTIONAL	boolean	save to log file
Schedule	OPTIONAL	existing file name	replaces default schedule
searchr_x	OPTIONAL	integer	search angles along x-axis, in degrees
searchr_y	OPTIONAL	integer	search angles along y-axis, in degrees
searchr_z	OPTIONAL	integer	search angles along z-axis, in degrees
sinc_width	OPTIONAL	integer	full-width in voxels
sinc_window	OPTIONAL	string	sinc window: rectangular, hanning, blackman
terminal_output	OPTIONAL	string	control terminal output: stream, allatonce, file, none
uses_qform	OPTIONAL	boolean	initialize using sform or qform
verbose	OPTIONAL	integer	verbose mode, 0 is least
wm_seg	OPTIONAL	file name	white matter segmentation volume needed by BBR cost function
wmcoords	OPTIONAL	file name	white matter boundary coordinates for BBR cost function
wmnorms	OPTIONAL	file name	white matter boundary normals for BBR cost function
out_file	OUTPUTS	exisitng file name	path/name of registered file
out_log	OUTPUTS	file name	path/name of output log
out_matrix_file	OUTPUT	existing file name	path/name of calculated affine transform

standard_reference_image