Usage¶

Command-Line Arguments¶

NiBetaSeries BIDS arguments

usage: nibs [-h] [-v] [-sm SMOOTHING_KERNEL] [-lp LOW_PASS]
            [-c CONFOUNDS [CONFOUNDS ...]] [-w WORK_DIR]
            [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
            [--session_label SESSION_LABEL] [-t TASK_LABEL]
            [--run_label RUN_LABEL] [-sp {MNI152NLin2009cAsym}]
            [--variant_label VARIANT_LABEL] [--exclude_variant_label]
            [--hrf_model {glover,spm,fir,glover + derivative,glover + derivative + dispersion,spm + derivative,spm + derivative + dispersion}]
            [-a ATLAS_IMG] -l ATLAS_LUT [--nthreads NTHREADS]
            [--use-plugin USE_PLUGIN] [--graph]
            bids_dir derivatives_pipeline output_dir {participant,group}

Positional Arguments¶

`bids_dir`	The directory with the input dataset formatted according to the BIDS standard.
`derivatives_pipeline`
	The pipeline that contains minimally preprocessed img, brainmask, and confounds.tsv
`output_dir`	The directory where the output directory and files should be stored. If you are running group level analysis this folder should be prepopulated with the results of theparticipant level analysis.
`analysis_level`	Possible choices: participant, group Level of the analysis that will be performed Multiple participant level analyses can be run independently (in parallel) using the same output_dir

Named Arguments¶

`-v, --version`	show program’s version number and exit
`--participant_label`
	The label(s) of the participant(s) 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.

Options for preprocessing¶

`-sm, --smoothing_kernel`
	select a smoothing kernel (mm)
`-lp, --low_pass`
	low pass filter (Hz)
`-c, --confounds`
	The confound column names that are to be included in nuisance regression. write the confounds you wish to include separated by a space
`-w, --work_dir`	directory where temporary files are stored

Options for selecting images¶

`--session_label`
	select a session to analyze
`-t, --task_label`
	select a specific task to be processed
`--run_label`	select a run to analyze
`-sp, --space_label`
	Possible choices: MNI152NLin2009cAsym select a bold derivative in a specific space to be used
`--variant_label`
	select a variant bold to process
`--exclude_variant_label`
	exclude the variant from FMRIPREP

Options for processing beta_series¶

`--hrf_model`	Possible choices: glover, spm, fir, glover + derivative, glover + derivative + dispersion, spm + derivative, spm + derivative + dispersion convolve your regressors with one of the following hemodynamic response functions
`-a, --atlas-img`
	input atlas nifti where each voxel within a “region” is labeled with the same integer and there is a unique integer associated with each region of interest
`-l, --atlas-lut`
	atlas look up table (tsv) formatted with the columns: index, regions which correspond to the regions in the nifti file specified by –atlas-img

Options to handle performance¶

`--nthreads, --n_cpus, -n-cpus`
	maximum number of threads across all processes
`--use-plugin`	nipype plugin configuration file

misc options¶

--graph

generates a graph png of the workflow