cmind.pipeline.cmind_fMRI_preprocess2

Functions

cmind_fMRI_preprocess2(output_dir, func_file) FMRI Preprocessing: Stage 2
cmind_feat_prep(output_dir, func_file, TR[, ...]) run additional Feat preprocessing steps
cmind.pipeline.cmind_fMRI_preprocess2.cmind_fMRI_preprocess2(output_dir, func_file, feat_params=None, TR=None, smooth=None, paradigm_hp=None, brain_thresh=None, perfusion_subtract=False, preprocess_case=None, slice_timing_file=None, usan_vol=None, output_tar=False, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]

FMRI Preprocessing: Stage 2

Parameters:

output_dir : str

directory in which to store the output

func_file : str

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

feat_params : str, optional

filename of a text (.csv) file containing parameters of the FEAT preprocessing

TR : float, optional

repetition time, TR (seconds). If not specified will be read from feat_params

smooth : float, optional

spatial smoothing (mm). If not specified will be read from feat_params

paradigm_hp : float, optional

high pass filter cutoff (seconds). If not specified will be read from feat_params

brain_thresh : float, optional

brain threshold (percent). If not specified will be read from feat_params

perfusion_subtract : bool, optional

if True, perform ASL surround subtraction. If not specified will be read from feat_params

preprocess_case : str or None, optional

placeholder that may be used in the future to apply different processing to different cases

slice_timing_file : str or None, optional

slice timing file

usan_vol : str or None, optional

filename of alternative usan_vol for susan smoothing. if not specified mean_func is used as in Feat

output_tar : bool, optional

compress the feat preprocessing folder into a .tar.gz archive

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:

filtered_func_data : str

filename corresponding to the filtered functional data

noise_est_file : str

noise_est.txt file corresponding to filtered_func_data

preproc_tarfile : str or None

.tar.gz archive where results were stored

feat_params_out : str

filename of a .csv file containing the preprocessing options that were used

prep_dir : str

directory where the preprocessed results were stored

Notes

Carries out spatial smoothing, bandpass temporal filtering, etc.

cmind.pipeline.cmind_fMRI_preprocess2.cmind_feat_prep(output_dir, func_file, TR, smooth=5, paradigm_hp=128, brain_thresh=10, use_OTSU=False, usan_vol=None, susan_bt_usan=None, perfusion_subtract=False, slice_timing_file=None, verbose=False, logger=None)[source]

run additional Feat preprocessing steps

Parameters:

output_dir : str

directory in which to store the output

func_file : str

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

TR : float

repetition time, TR (seconds)

smooth : float, optional

spatial smoothing (mm)

paradigm_hp : float, optional

high pass filter cutoff (seconds)

brain_thresh : float, optional

brain threshold (percent).

use_OTSU : bool, optional

NOTE: if skimage.filter.threshold_otsu is found, brain_thresh is ignored and OTSU threshold is used instead

usan_vol : str, optional

filename of alternative usan_vol for susan smoothing. if not specified mean_func is used as in Feat

susan_bt_usan : float, optional

brightness threshold for susan_smooth

perfusion_subtract : bool, optional

if True, perform ASL surround subtraction

slice_timing_file : str, optional

slice timing file

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:

filtered_func_data : str

filename of the filtered 4D functional data

noise_est_file : str

filename of the noise estimation parameters

preproc_tarfile : str

filename of the .tar.gz archive containing the preprocessing results

See also

cmind_feat_preprocess2

Notes

Carries out spatial smoothing, bandpass temporal filtering, etc. Called by cmind_feat_preprocess2