conf_driv.json

{
    "general": {
        "fslRootDir": "/usr/local/fsl",
        "freesurferRootDir": "/Applications/freesurfer/7.4.1",
        "templates": [
            "aparc",
            "lausanne120",
            "schaefer100-yeo7"
        ],
        "reconstructionMethods": [
            "DTI",
            "CSD",
            "CSD_DTI"
        ],
        "reconstructionSteps": [
            "structural_preprocessing",
			"parcellation",
			"collect_region_properties",
			"reconstruction_diffusion",
			"reconstruction_fibers",
			"reconstruction_fiber_properties",
			"reconstruction_network"
        ],
        "maxNumberCompThreads": 1,
        "freesurferDir": "../../derivatives/freesurfer/ses-01/SUBJECT",
        "outputDir": "../../derivatives/cato/ses-01/SUBJECT/DWI_processed"
    },
    "structural_preprocessing": {
        "rawBvalsFile": "ses-01/dwi/SUBJECT_ses-01_dwi.bval",
        "rawBvecsFile": "ses-01/dwi/SUBJECT_ses-01_dwi.bvec",
        "dwiFile": "ses-01/dwi/SUBJECT_ses-01_dwi.nii.gz",
        "dwiB0ReversedFile": "",
        "dwiReversedFile": "",
        "synb0File": "../../derivatives/synb0-DISCO/ses-01/SUBJECT/b0_all.nii.gz",
        "preprocessingScript": "TOOLBOXDIR/structural_preprocessing/preprocess_topup_eddy_synb0.sh",
        "eddyVersion": "eddy",
        "indexFile": "../../derivatives/cato/ses-01/SUBJECT/DWI_processed/index.txt",
        "acqpFile": "../../../../acq_driv.txt"
    },
    "parcellation": {
        "forceFreesurferOverwrite": false
    },
    "reconstruction_diffusion": {
        "exportNifti": {
            "exportNifti": true,
            "measures": [
                "fractional anisotropy",
                "axial diffusivity",
                "radial diffusivity",
                "mean diffusivity"
            ]
        }
    },
    "reconstruction_fibers": {
        "NumberOfSeedsPerVoxel": 8,
        "minFA": 0.1,
        "maxAngleDeg": 45,
        "startRegions": [
            2,
            41,
            251,
            252,
            253,
            254,
            255
        ],
        "forbiddenRegions": [
            1,
            6,
            7,
            8,
            40,
            45,
            46,
            47
        ],
        "stopRegions": [
            16,
            28,
            60
        ]
    },
    "reconstruction_network": {
        "minLengthMM": 0
    }
}