Usage

Start by importing atlascorr.

atlas_correlations

usage: atlascorr [-h] --deriv-pipeline DERIV_PIPELINE [--atlas-img ATLAS_IMG]
                 --atlas-lut ATLAS_LUT [--confounds CONFOUNDS [CONFOUNDS ...]]
                 [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                 [--hp HP] [--lp LP] [--variant VARIANT] [--run RUN]
                 [--session SESSION] [--task TASK]
                 {participant,group}

Positional Arguments

analysis_level

Possible choices: participant, group run participant level analysis, or aggregate group level results

Named Arguments

--deriv-pipeline, -d
	input derivative directory (e.g. fmriprep). I assume the inputs are in MNI space.
--atlas-img, -a
	input atlas nifti
--atlas-lut, -l
	atlas look up table formatted with the columns: index, regions
--confounds, -c
	names of confounds to be included in analysis
--participant_label, --participant-label
	one or more participant identifiers with the sub- prefix removed
--hp	highpass filter to apply to the data
--lp	lowpass filter to apply to the data
--variant	only analyze files with a specific variant label
--run	only analyze files with a specific run label
--session	only analyze files with a specific session label
--task	only analyze files with a specific task label