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 |
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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
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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)