.. _flirt_params_file: flirt_params ------------ .. _FLIRT_params_table: .. list-table:: Available Keys for the flirt_params in the flirt control JSON file. Input and output files do not need specified here. :widths: 30 15 15 40 :header-rows: 1 * - **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** .. _std_reference_inputs: .. list-table:: Standard reference image input dictionary keys. :widths: 30 15 15 40 :header-rows: 1 * - **Key Name** - **Required?** - **Data Type** - **Description** * - in_file - REQUIRED - exisitng file name - name of input image * - ref_file - REQUIRED - existing file name - name of reference image * - affine_file - OPTIONAL - exisitng file name - name of file containing affine transform * -