Usage Notes

Command-Line Arguments

[-h] --input_dir INPUT_DIR --output_dir OUTPUT_DIR --group
            {participant,batch}
            [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
            [--session_label SESSION_LABEL [SESSION_LABEL ...]]
            [--preprocessing_type {HCP,fmriprep}]
            [--use_ICA_outputs {Yes,yes,No,no}]
            [--combine_resting_scans {Yes,yes,No,no}]
            [--smoothing SMOOTHING] --parcellation_file PARCELLATION_FILE
            --parcellation_name PARCELLATION_NAME --seed_ROI_name
            SEED_ROI_NAME [SEED_ROI_NAME ...]
            [--seed_handling {together,separate}]
            [--seed_analysis_output {dense,parcellated}]
            [--motion_confounds {NONE,Movement_Regressors,Movement_Regressors_dt,Movement_RelativeRMS,Movement_RelativeRMS_mean,Movement_AbsoluteRMS,Movement_AbsoluteRMS_mean,dvars,fd}]
            [--reg_name {NONE,MSMAll_2_d40_WRN}]
            [--text_output_format {CSV,csv,none,NONE}] [--num_cpus NUM_CPUS]
            [--statistic {correlation,regression}]

Required Arguments

--input_dir INPUT_DIR
	The directory where the preprocessed derivative needed live
--output_dir OUTPUT_DIR
	The directory where the output files should be stored.
--group GROUP	Whether to run this participant by participant or the entire group. Choices are “participant” or “batch”. If participant by participant “–participant_label” and ” –session_label” must be specified
--parcellation_file PARCELLATION_FILE
	The CIFTI label/atlas file to use or used to parcellate the brain.
--parcellation_name PARCELLATION_NAME
	Shorthand name of the CIFTI label file.
--seed_ROI_name SEED_ROI_NAME
	Space separated list of ROI name/s from CIFTI label file to be used as the seed ROI/s. The exact ROI from the label file must be known!

Optional Arguments

-h, --help	show this help message and exit
--participant_label PARTICIPANT_LABEL
	The label of the participant that should be analyzed. The label corresponds to sub-<participant_label> from the BIDS spec (so it does not include “sub-“). If this parameter is not provided all subjects should be analyzed. Multiple participants can be specified with a space separated list.
--session_label SESSION_LABEL
	The label of the session that should be analyzed. The label corresponds to ses-<session_label> from the BIDS spec (so it does not include “ses-“). If this parameter is not provided all sessions within a subject should be analyzed.
--preprocessing_type PREPROCESSING_TYPE
	BIDS-apps preprocessing pipeline run on data. Choices include “HCP” and “fmriprep”. Default: “HCP”.
--use_ICA_outputs USE_ICA_OUTPUTS
	Use ICA (whether FIX or AROMA) outputs in seed analysis. Choices include “Y/yes” or “N/no”. Default: “Yes”.
--combine_resting_scans COMBINE_RESTING_SCANS
	If multiple of the same resting state BIDS file type exist should they be combined prior seed analysis? Choices include “Y/yes” or “N/no”. Default “No”.
--smoothing SMOOTHING
	What FWHM smoothing (in mm) to apply to final output, only applies to SBA with dtseries. Default: 4
--seed_handling SEED_HANDLING
	Of the ROI/s you have provided do you want to treat them as together (i.e. averaging ROIs together), or separate (run separate seed based analyses for each ROI)? Choices are “together”, or “separate”. Default: “separate”.
--seed_analysis_output SEED_ANALYSIS_OUTPUT
	The output of the seed based analysis. Choices are “dense” (i.e. dtseries.nii) and “parcellated” (i.e. ptseries.nii)). Default: “parcellated”.
--motion_confounds MOTION_CONFOUNDS
	What type of motion confounds to use, if any. Note only works in combination with “–statistic regression”. Choices are “Movement_Regressors” (motion rotation angles and translations in mm), “Movement_Regressors_dt” (detrended motion rotation angles and translations in mm), “Movement_Regressors_demean” (demeaned motion rotation angles and translations in mm) “Movement_RelativeRMS” (RMS intensity difference of volume N to the reference volume), “Movement_RelativeRMS_mean” (square of RMS intensity difference of volume N to the reference volume), “Movement_AbsoluteRMS” (absolute RMS intensity difference of volume N to the reference volume, “Movement_AbsoluteRMS_mean” (square of absolute RMS intensity difference of volume N to the reference volume), “dvars” ( RMS intensity difference of volume N to volume N+1 (see Power et al, NeuroImage, 59(3), 2012)), “fd” ( frame displacement (average of rotation and translation parameter differences - using weighted scaling, as in Power et al.))
--reg_name REG_NAME
	What type of registration do you want to use? Choices are “MSMAll_2_d40_WRN” and “NONE”. Default: “MSMAll_2_d40_WRN”.
--text_output_format TEXT_OUTPUT_FORMAT
	What format should the text output be in? Choices are “CSV” or “NONE”. Default: “CSV”.
--num_cpus NUM_CPUS
	How many concurrent CPUs to use. Default: “1”.
--statistic STATISTIC
	Strategy to calculate functional connectivity. Choices are “correlation”, and “regression” Default: “correlation”