average-measure

Synopsis

average-measure [-h] [-n NAME [NAME ...]]
[-roi-name ROI_NAME [ROI_NAME ...]] [-size SIZE_TABLE]
[-o MEAN_TABLE] [-sdev SDEV_TABLE] [-var VAR_TABLE]
[-se SE_TABLE] [-u] -r ROI [ROI ...] [-d DELIM]
[-s SCALE] [-digits DIGITS] [-preload] [-transpose]
[-header] [-id ID_NAME] [-noid] [-a]
measure [measure ...]

Description

Average voxel-wise measure within each region of interest (ROI).

Arguments

measure

Input image(s) of voxel-wise scalar measure.

Command options

-h, --help

show this help message and exit

-n NAME [NAME ...], -name NAME [NAME ...], -names NAME [NAME ...], --name NAME [NAME ...], --names NAME [NAME ...]

Names of input measures. Input file name excluding file name extension is used by default.

-roi-name ROI_NAME [ROI_NAME ...], -roi-names ROI_NAME [ROI_NAME ...], --roi-name ROI_NAME [ROI_NAME ...], --roi-names ROI_NAME [ROI_NAME ...]

Names of ROIs. By default, one-based ROI IDs are generated.

-size SIZE_TABLE, -roi-size SIZE_TABLE, --size SIZE_TABLE, --roi-size SIZE_TABLE

Write sizes (sum of weights) of ROIs to specified file.

-o MEAN_TABLE, -mean MEAN_TABLE, -output MEAN_TABLE, -table MEAN_TABLE, --mean MEAN_TABLE, --output MEAN_TABLE, --table MEAN_TABLE

Write mean values to specified table

-sdev SDEV_TABLE, -stdev SDEV_TABLE, -stddev SDEV_TABLE, -standard-deviation SDEV_TABLE, --sdev SDEV_TABLE, --stdev SDEV_TABLE, --stddev SDEV_TABLE, --standard-deviation SDEV_TABLE

Write standard deviation of weighted measurements to specified file.

-var VAR_TABLE, -variance VAR_TABLE, --var VAR_TABLE, --variance VAR_TABLE

Write variance of weighted measurements to specified file.

-se SE_TABLE, -standard-error SE_TABLE, --se SE_TABLE, --standard-error SE_TABLE

Write standard error of weighted mean to specified file.

-u, -unbiased, --unbiased

When computing second moments, apply Bessel’s correction.

-r ROI [ROI ...], -region ROI [ROI ...], -roi ROI [ROI ...], -roi-path ROI [ROI ...], --region ROI [ROI ...], --roi ROI [ROI ...], --roi-path ROI [ROI ...]

Binary mask or segmentation probability map of ROI(s).

-d DELIM, -delim DELIM, -delimiter DELIM, --delim DELIM, --delimiter DELIM

String/character used to delimit table entries.

-s SCALE, -scale SCALE, --scale SCALE

Common scaling factor by which to multiply input values.

-digits DIGITS, -precision DIGITS, --digits DIGITS, --precision DIGITS

Number of digits after the decimal point.

-preload, --preload

Read each input image only once. Requires enough memory to preload all measures into memory.

-transpose, --transpose

Transpose output table s.t. each row corresponds to an input measure

-header, --header

Print table header

-id ID_NAME, --id ID_NAME

Header value of ID column

-noid, --noid

Do not print ID column

-a, -append, --append

Append results to existing table.