QualityIndex brick¶

Computes a quality index for each sub-brick (3D volumes for each TR) in a 3D+time dataset using AFNI 3dTqual¶

The output is a 1D time series with the index for each sub-brick.

Mandatory inputs parameters:

in_file (a string representing an existing file)

Input image.

ex. '/home/username/data/derived_data/reg_func_valid.nii'

Optional inputs with default value parameters:

autoclip (a boolean, optional, default value is False)
Clip off small voxels. Mutually exclusive with mask.
ex. False
automask (a boolean, optional, default value is True)
Clip off small voxels. Mutually exclusive with mask
ex. True
interval (a boolean or an integer, optional, default value is False)
Write out the median + 3.5 MAD of outlier count with each timepoint.
ex. False
out_prefix (a string, optional, default value is ‘QI’)
Specify the string to be prepended to the filename of the output file.
ex. 'QI_'
quadrant (a boolean or an integer, optional, default value is False)
Similar to spearman parameter, but using 1 minus the quadrant correlation coefficient as the quality index.
ex. False
spearman (a boolean or an integer, optional, default value is False)
Quality index is 1 minus the Spearman (rank) correlation coefficient of each sub-brick with the median sub-brick.
ex. False

Optional inputs:

mask_file (a string representing an existing file, optional)
Mask image. Compute correlation only across masked voxels. Mutually exclusive with automask and autoclip.
ex. '/home/username/data/derived_data/automask_mean_reg_func_valid.nii'
polort (an integer, optional)
Detrend each voxel timeseries with polynomials. Default value is Undefined (i.e parameter not used)
ex. 3

Outputs parameters:

out_file (a strings representing a file)

Out file.

ex. '/home/username/data/derived_data/outliers_reg_func_valid.out'

Useful links: