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}]
[--summarymethod {mean,median,sum}] [--ignorezeros]
[--regionlistfile REGIONLISTFILE]
[--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”
- --summarymethod
Possible choices: mean, median, sum
Method to summarize a region. Choices are ‘mean’ (default), ‘median’, and ‘sum’.
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.
- --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