atlasaverage

Description:

Average data within atlas regions.

Inputs:

datafile - The name of the 3 or 4D nifti file with the data to be averaged over atlas regions. templatefile - The name of the atlas region NIFTI file outputroot - The root name of the output files.

Outputs:

A csv file containing the summary metrics for each region in the atlas.

Usage:

Average data within atlas regions.

usage: atlasaverage [-h] [--normmethod {none,pct,var,std,p2p}]
                    [--numpercentiles NPCT]
                    [--summarymethod {mean,median,sum,std,MAD,CoV}]
                    [--ignorezeros] [--regionlistfile REGIONLISTFILE]
                    [--regionlabelfile REGIONLABELFILE]
                    [--includemask MASK[:VALSPEC]]
                    [--excludemask MASK[:VALSPEC]] [--extramask MASK]
                    [--headerline] [--datalabel LABEL] [--debug]
                    datafile templatefile outputroot

Positional Arguments

datafile

The name of the 3 or 4D nifti file with the data to be averaged over atlas regions.

templatefile

The name of the atlas region NIFTI file

outputroot

The root name of the output files.

Named Arguments

--normmethod

Possible choices: none, pct, var, std, p2p

Normalization to apply to input timecourses (in addition to demeaning) prior to combining. Choices are ‘none’ (no normalization, default), ‘pct’ (divide by mean), ‘var’ (unit variance), ‘std’ (unit standard deviation), and ‘p2p’ (unit range).

Default: 'none'

--numpercentiles

Number of evenly spaced percentiles between 0 and 100 (not including the end points) to calculate in each region. For example, If NPCT = 1, calculate the 0th, 50th, and 100th percentiles.

Default: 1

--summarymethod

Possible choices: mean, median, sum, std, MAD, CoV

Method to summarize the voxels in a region. Choices are ‘mean’ (default), ‘median’, ‘sum’, ‘std’, ‘MAD’, and ‘CoV’.

Default: 'mean'

--ignorezeros

Zero value voxels will not be included in calculation of summary statistics.

Default: False

--regionlistfile

The name of of a text file containing the integer region numbers to summarize, one per line. Values that do not exist in the atlas will return NaNs.

--regionlabelfile

The name of of a text file containing the labels of the regions, one per line. The first line is the label integer value 1, etc.

--includemask

Only use atlas voxels that are also in file MASK in calculating the region summaries (if VALSPEC is given, only voxels with integral values listed in VALSPEC are used).

--excludemask

Do not use atlas voxels that are also in file MASK in calculating the region summaries (if VALSPEC is given, voxels with integral values listed in VALSPEC are excluded).

--extramask

Additional mask to apply select voxels for region summaries. Zero voxels in this mask will be excluded.

--headerline

Add a header line to the text output summary of 3D files.

Default: False

--datalabel

Label to add to the beginning of the text summary line.

--debug

Output additional debugging information.

Default: False