cmind.pipeline.cmind_fMRI_level1_stats

Functions

cmind_fMRI_level1_stats(output_dir, ...[, ...]) Utility to run FEAT stats/poststats processing equivalent
cmind_feat_stats(prep_dir, stats_dir, ...[, ...]) utility to run “stats” portion of FEAT processing
cmind.pipeline.cmind_fMRI_level1_stats.cmind_fMRI_level1_stats(output_dir, FSF_template, prep_dir, stats_dir=None, lvl1_stats_case='', nuisance_file='', feat_params=None, z_thresh=None, prob_thresh=None, thresh=None, output_tar=False, CMIND_specific_figures=False, omit_poststats=True, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]

Utility to run FEAT stats/poststats processing equivalent

Parameters:

output_dir : str

directory in which to store the output

FSF_template : str

design.fsf template filename

prep_dir : str

specify location where cmind_fMRI_preprocess2.py output is located

stats_dir : str, optional

specify location where stats output should go (or is already located)

lvl1_stats_case : str, optional

may be used in future to apply different processing to different cases

nuisance_file : str, optional

path to a text file with one nuisance regressor per column

feat_params : str, optional

filename to a .csv file containing feat parameters listed as key,value pairs. If z_thresh, prob_thresh, or thresh are explicitly passed in, those values will override the ones in the feat_params file. Typically feat_params should be the preproc_options_file output by cmind_fMRI_preprocess2

z_thresh : float, optional

initial z threshold to use when determining clusters. unused if thresh!=2

prob_thresh : float, optional

probability threshold for voxelwise or cluster significance

thresh : {0,1,2}, optional

0 = uncorrected, 1 = voxel-based (FWE corrected), 2 = cluster-based

output_tar : bool, optional

if true, generate .tar.gz versions of stats and poststats folders

CMIND_specific_figures : bool, optional

generate additional figures for the CMIND paradigm results. set this to False if the data is not from the CMIND project

omit_poststats : bool, optional

it True, run stats only without poststats thresholding

generate_figures : bool,optional

if true, generate overlay images summarizing the registration

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:

stats_tarfile : str or None

filename of the .tar.gz file containing the stats output

poststats_tarfile : str or None

filename of the .tar.gz file containing the poststats output

output_dir : str

Feat directory where the analysis was performed

stats_dir : str

stats output folder

poststats_dir : str or None

poststsats output folder

See also

cmind_fMRI_outliers

Notes

cmind_fMRI_outliers should be used to generate a file for extra_confounds FEAT stats subdirectory will be created as a softlink to stats_dir

For the C-MIND study, CMIND-specific figures will be created for the following lvl1_stats_case values: Feat_BOLD_Stories Feat_BOLD_Sentences Feat_ASL_Stories Feat_ASL_Sentences

cmind.pipeline.cmind_fMRI_level1_stats.cmind_feat_stats(prep_dir, stats_dir, FSF_template, smooth=5, brain_thresh=10, perfusion_subtract=False, extra_confounds=None, verbose=False, logger=None)[source]

utility to run “stats” portion of FEAT processing

Parameters:

prep_dir : str

FEAT output directory from preprocessing with cmind_ffMRI_preprocess2

stats_dir : str

output directory to store the stats images in

smooth : str, optional

spatial smoothing (mm)

brain_thresh : str, optional

brain threshold

FSF_template : bool

FSF template (e.g. design.fsf)

perfusion_subtract : bool, optional

maximum allowed width in pixels of the output overlay images

extra_confounds : str, optional

text file containing one confound ev per column

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)