cmind.pipeline.cmind_fMRI_outliers¶
Functions
binstr2dec (binstr) |
Convert a binary string such as “0100101” to its decimal (base 10) |
cmind_fMRI_outliers (output_dir, ...[, ...]) |
Detect outlier timepoints in fMRI timeseries and generate nuisance |
orthogonalize (ts1, ts2) |
orthogonalize ts1 with respect to ts2 |
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cmind.pipeline.cmind_fMRI_outliers.
binstr2dec
(binstr)[source]¶ Convert a binary string such as “0100101” to its decimal (base 10) representation
Parameters: binstr : str
binary string to convert
Returns: decval : int
decimal value corresponding to binstr
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cmind.pipeline.cmind_fMRI_outliers.
cmind_fMRI_outliers
(output_dir, contrast_of_interest, regBBR_ref, WM_pve_vol, GM_pve_vol, CSF_pve_vol, vol_file_niigz, filtered_func_data, motion_parfile, unfiltered_design_matrix, FSF_template, noise_est_file, HRtoLR_Affine=None, HRtoLR_Warp=None, Nproc_max=1, generate_figures=True, ForceUpdate=False, verbose=False, logger=None)[source]¶ Detect outlier timepoints in fMRI timeseries and generate nuisance regressors
Parameters: output_dir : str
directory in which to store the output
contrast_of_interest : int or list of int
which contrast in FSF_template is of primary interest? Note: Unlike in the FSL GUI, contrast numbering begins from 0!. If this is a list the minimum effect size among the contrasts in the list will be used during the computation
regBBR_ref : str
filename of the regBBR reference image
WM_pve_vol : str
WM partial volume estimate from structural processing
GM_pve_vol : str
GM partial volume estimate from structural processing
CSF_pve_vol : str
CSF partial volume estimate from structural processing
vol_file_niigz : str
unfiltered 4D fMRI timeseries to process
filtered_func_data : str
smoothed and temporal filtered 4D fMRI timeseries file to process
motion_parfile : str
The 6 column motion parameter (.par) file from mcflirt
unfiltered_design_matrix : str
The (unfiltered) Feat design matrix corresponding to vol_file_niigz
FSF_template : str
THE .fsf template corresponding to vol_file_niigz
noise_est_file : str
The noise_est.txt file from cmind_fMRI_preprocess2.py
HRtoLR_Affine : str, optional
filename for the affine transform from functional->structural space
HRtoLR_Warp : str, optional
fieldmap corrected warp from functional->structural space
Nproc_max : int, optional
maximum number of processes to launch simultaneously
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: default_confound_file : str
confound file with 6 motion + outliers
best_confound_file : str
optimal confound file
worst_confound_file : str
“worst” confound file
mcf06_confound_file : str
6 motion parameters confound file
FSL_outliers_txt : str
outliers confound file
Notes
For the “optimal” nuisance regressor evaluation the following regressor sets are considered:
- mean CSF regressor (orthogonalized w.r.t. ASL/BOLD baseline)
- mean WM regressor (orthogonalized w.r.t. ASL/BOLD baseline)
- 6 rigid body motion parameters
- squares of the 6 motion parameters
- derivatives of the 6 motion parameters
- squares of the derivatives of the 6 motion parameters
- outlier regressors
PCA is also applied to the combined set of regressors and thresholds for 75, 90, 95 and 99 percent of explained variance are applied. These four PCA regressor sets are evaluated in addition to the 2**7=128 possible combinations of the 7 regressor sets mentioned above.