cmind.pipeline.cmind_fMRI_preprocess

Functions

cmind_fMRI_preprocess(output_dir, BOLD_vol) run coregistration of ASL and BOLD timeseries
cmind.pipeline.cmind_fMRI_preprocess.cmind_fMRI_preprocess(output_dir, BOLD_vol, ASL_vol=None, paradigm_name='', ANTS_bias_cmd='', UCLA_flag=False, fsl_motion_outliers_cmd=None, FORCE_SINGLEPROCESS=False, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]

run coregistration of ASL and BOLD timeseries

Parameters:

output_dir : str

directory in which to store the output

BOLD_vol : str

filename of the NIFTI/NIFTI-GZ BOLD 4D timeseries

ASL_vol : str or None, optional

filename of the NIFTI/NIFTI-GZ ASL 4D timeseries

paradigm_name : str, optional

output filenames will incorporate this name. may also be used in the future to apply different processing streams to different cases. e.g. {‘Stories’,’Sentences’,’‘}

ANTS_bias_cmd : str, optional

pathname to the ANTs bias field correction binary

UCLA_flag : bool, optional

if True, ASL labeling order is tag, control, tag, ... if False, ASL labeling order is control, tag, control...

fsl_motion_outliers_cmd : str, optional

path to the fsl_motion_outliers_cmd_v2 shell script. If not specified will try to guess it relative to the python script location.

FORCE_SINGLEPROCESS : bool, optional

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

generate_figures : bool, optional

if true, generate additional summary images

ForceUpdate : bool,optional

if True, rerun and overwrite any previously existing results

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:

ASL_mcf_vol : str or None

motion corrected ASL timeseries

BOLD_mcf_vol : str

motion corrected BOLD timeseries

meanCBF_N4_vol : str or None

mean control-tag image from ASL timeseries

meanBOLD_N4_vol : str

mean image from BOLD timeseries

motion_parfile_ASL : str or None

ASL motion parameters

motion_parfile_BOLD : str

BOLD motion parameters

Notes

By default will try to run two instances of mcflirt simultaneously (for ASL and BOLD)