Spikes brick¶

Computes the number of spikes¶

Adapted from mriqc functional workflow (spikes_mask function and Spikes class).

Mandatory inputs parameters:

in_file (a string representing an existing file)
Input bold image (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/func.nii'

Optional inputs with default value parameters:

detrend (a boolean, optional, default value is False)
Detrend data.
ex. False
no_zscore (a boolean, optional, default value is True)
Do not zscore
ex. True
out_prefix (a string, optional, default value is ‘spikes’)
Prefix of the output image.
ex. 'spikes_'
skip_frames (an integer, optional, default value is 0)
Number of frames to skip in the beginning of the time series.
ex. 0
spike_thresh (a float, optional, default value is 6.0)
z-score to call one timepoint of one axial slice a spike.
ex. 6.0

Outputs parameters:

out_file (a strings representing a file)
Out file with all the spkies detected.
ex. '/home/username/data/derived_data/spikes_func.out'

Useful links: