config_functional_default.json

{
	"general":{
		"fslRootDir":"/Applications/fsl/5.0.10",
		"freesurferRootDir": "/Applications/freesurfer/6.0.0", 		
		"parameterPropertiesFile": "functionalParameterProperties.xlsx",
		"templates": ["aparc", "economo", "BB50human", "lausanne120", "lausanne250"],
		"reconstructionSteps":{ 
			"functional_preprocessing": true,
			"parcellation": true,
			"collect_region_properties": true,
			"compute_motion_metrics": true,
			"reconstruction_functional_network": true
		},
		"freesurferDir": "T1/SUBJECT_FS",
		"templatesDir": "TOOLBOXDIR/templates",
		"ROIsFile": "TEMPLATESDIR/TEMPLATE/ROIs_TEMPLATE.txt",
		"outputDir": "fMRI_processed",
		"logFile": "OUTPUTDIR/functional_pipeline.log",
		"statusFile": "OUTPUTDIR/functional_pipeline.STATUS",		
		"computedConfigFile": "OUTPUTDIR/functional_configuration.json",
		"maxNumberCompThreads": 1,
		"TEMPDIR": "",
		"fmriProcessedTMPFile": "TEMPDIR/SUBJECT_fmri.nii"
	},
	"functional_preprocessing":
	{
		"fmriFile": "fMRI/SUBJECT_fmri.nii.gz",
		"fmriProcessedFile": "OUTPUTDIR/SUBJECT_fmri.nii.gz",
		"motionParametersFile": "OUTPUTDIR/SUBJECT_motion_parameters.par",
		"fmriReferenceFile": "OUTPUTDIR/SUBJECT_ref.nii.gz",
		"registrationMatrixFile": "OUTPUTDIR/SUBJECT_ref_to_freesurfer.dat",
		"segmentationFile": "OUTPUTDIR/SUBJECT_aseg_ref.nii.gz",
		"sliceTimingCorrection":true,
		"sliceTimerOptions": "",
		"fmriInfo": "",
		"preprocessingScript": "TOOLBOXDIR/functional_preprocessing/preprocess_default.sh"
	},
	"parcellation":{
		"templateScript": "TEMPLATESDIR/TEMPLATE/parcellate_TEMPLATE.sh",
		"parcellationFile": "OUTPUTDIR/SUBJECT_TEMPLATE+aseg_ref.nii.gz",
		"lutFile": "TEMPLATESDIR/TEMPLATE/TEMPLATE.annot.ctab",
		"matchROIs": true,		
		"forceFreesurferOverwrite": false
	},
	"collect_region_properties":{
		"statsLhFile": "FREESURFERDIR/stats/lh.TEMPLATE.stats",
		"statsRhFile": "FREESURFERDIR/stats/rh.TEMPLATE.stats",
		"statsSubFile": "FREESURFERDIR/stats/aseg.stats",
		"regionPropertiesFile": "OUTPUTDIR/SUBJECT_region_properties_TEMPLATE.mat"
	},
	"compute_motion_metrics":{
		"motionMetricsFile": "OUTPUTDIR/SUBJECT_motion_metrics.mat"
	},
	"reconstruction_functional_network":{
		"methodDescription": "scrubbed_0.01-0.1",
		"reconstructionMethod": "corr",
		"connectivityMatrixFile": "OUTPUTDIR/SUBJECT_connectivity_METHOD_TEMPLATE.mat",
		"timeSeriesFile": "OUTPUTDIR/SUBJECT_time_series_METHOD_TEMPLATE.mat",
        "minRepetitionTime": 100,
		"regression":{
			"regressionMask": [24,2,41,251,252,253,254,255],
			"globalMeanRegression": false
		},
		"bandpass_filter":{
			"filter": true,
			"frequencies": [0.01, 0.1]
		},
		"truncateFrames": 5,
		"scrubbing":{
			"scrubbing": true,
			"maxFD": 0.25, 
			"maxDVARS": 1.5, 
			"minViolations": 2,
			"backwardNeighbors": 1,
			"forwardNeighbors": 0
		},
		"saveTimeSeries": true
	}
}