cmind.utils.fsl_mcflirt_opt_ASLBOLD

mcflirt motion correction for simultaneous ASL/BOLD data

Functions

fsl_mcflirt_opt_ASLBOLD(ASLinput_name, ...) Utility that tries to improve the robustness of mcflirt by running in 3 stages:
cmind.utils.fsl_mcflirt_opt_ASLBOLD.fsl_mcflirt_opt_ASLBOLD(ASLinput_name, BOLDinput_name, cost_type='normcorr', out_name_ASL='', out_name_BOLD='', FORCE_SINGLEPROCESS=False, output_dir=None, verbose=False, logger=None)[source]

Utility that tries to improve the robustness of mcflirt by running in 3 stages: This version runs ASL and BOLD registrations in parallel, forcing the same reference frame to be used

Parameters:

ASLinput_name : str

ASL 4D NIFTI or NIFTI-GZ volume

BOLDinput_name : str

BOLD 4D NIFTI or NIFTI-GZ volume

cost_type : {‘normcorr’,’mutualinfo’,’woods’,’corratio’,’normmi’,’leastsquares’}, optional

cost function used by mcflirt (default = ‘normcorr’)

out_name_ASL : str, optional

output filename to be used for the ASL motion-corrected timeseries

out_name_BOLD : str, optional

output filename to be used for the BOLD motion-corrected timeseries

output_dir : str, optional

if None, output will be stored in current working directory via os.getcwd()

FORCE_SINGLEPROCESS : bool, optional

if False will try to run ASL & BOLD motion correction in parallel via multiprocessing

verbose : bool, optional

print additional output (to terminal and log)

logger : logging.Logger or str, optional

logging.Logger object (or string of a filename to log to)

Returns:

out_name_ASL : str

output filename of the ASL motion-corrected timeseries

out_name_BOLD : str

output filename of the BOLD motion-corrected timeseries

Notes

The mcflirt stages run are: 1.) Fast initial registration to initial frame without sinc interpolation to find the frame closest to mean position 2.) Rerun mcflirt using this “optimal” reference frame and with sinc interpolation to reduce blurring 3.) Take a timeseries average of the reference frames and then run mcflirt a 3rd time using this high SNR timeseries average as the reference

mcflirt will duplicate the top and bottom slice during the calculations to allow some corrections to be made to the edge slices

cost_type options are: normcorr (default), mutualinfo, woods, corratio, normmi, leastsquares