config json file

The config.json file controls everything the container will do.

Fields

numberOfNodes:

{ "description": "AFQ: The number of nodes to represent each fiber.", "default": 100, "type": "integer" }

"fiberWeighting":

{ "description": "RTP: Set the amount of weighting that will be applied when calculating tract profiles. 0 means that each fiber contributes equally. 1 means that we apply gaussian weighting where each fibers contribution to the measurement at a node is weighted by its gaussian distance from the tract core. Values greater than 1 mean that the core of the tract is weighted more heavily and fibers further from the core are weighted less heavily (faster fall off than a gaussian). See ComputeTractProperties.", "default": 1, "type": "integer" }

"track_faFodThresh":

{ "description": "MRTRIX: Stopping criteria when tracking, FA for DTI and FOD for CSD. Mrtrix uses defaults depending on the algo and depending on the algo these number will refer to FA or FOD. If 999 use the defaults, otherwise use the value here. See mrTrix docs for defaults", "default": 999, "type": "number" },

"track_faMaskThresh":

{ "description": "MRTRIX: FA mask threshold from which to initialize tracking. It is used to create the wmMask that is used to seed the whole brain connectome in mrTrix", "default": 0.3, "type": "number" },

"mrtrix_mrTrixAlgo":

{ "description": "MRTRIX: Tracking algorithm for mrTrix's tckgen. Options are: iFOD1, iFOD2, SD_STREAM, Tensor_Det, Tensor_prob. DEFAULT='iFOD2'", "default": "iFOD2", "type": "string" }

"mrtrix_useACT":

{ "description": "MRTRIX: Use ACT for tracking. DEFAULT=False", "default": false, "type": "boolean" },

"mrtrix_autolmax":

{ "description": "MRTRIX: Calculate lmax automatically from number of directions. DEFAULT=True", "default": false, "type": "boolean" },

"mrtrix_lmax":

{ "description": "MRTRIX: specify lmax for CSD. Only used if mrtrix_autolmax==0. DEFAULT=6", "default": 6, "type": "integer" },

"get_vofparc":

{ "description": "If conditions are met (whole brain tractogram is created and arcuate fasciculus is tracked), obtain VOF and pARC bundles. DEFAULT=false", "default": false, "type": "boolean" },

"sift_runSift":

{ "description": "SIFT: Run SIFT algorithm. DEFAULT=true", "default": true, "type": "boolean" },

"sift_nFibers":

{ "description": "SIFT: Reduce whole brain tractogram until this number of fibers. DEFAULT=500000", "default": 500000, "type": "number" },

"life_runLife":

{ "description": "LiFE: Run LiFE algorithm. DEFAULT=false", "default": false, "type": "boolean" },

"life_saveOutput":

{ "description": "LiFE: Save outputs from LiFE algorithm. DEFAULT=true", "default": false, "type": "boolean" },

"life_discretization":

{ "description": "LiFE: Discretization parameter (this parameter defines the resolution of the Phi tensor in describing the orientation of the fascicles in the connectome (number of orientations encoded in Phi, more specifically the size of Phi in mode 1) DEFAULT=360", "default": 360, "type": "number" },

"life_num_iterations":

{ "description": "LiFE: Number of iterations for LiFE algorithm. DEFAULT=10", "default": 10, "type": "number" },

"life_test":

{ "description": "LiFE: Run LiFE in test mode. DEFAULT=False", "default": false, "type": "boolean" },

"life_writePDB":

{ "description": "LiFE: Write fibers out in PDB. This is a legacy format for the program Quench. DEFAULT=False", "default": false, "type": "boolean" },

"ET_numberFibers":

{ "description": "ET: Number of fibers to generate in each tractotram. As many tractograms as specified with ET_maxlength and ET_angleValues number of pairs will be generated and concatenated. DEFAULT=200000", "default": 200000, "type": "number" },

"ET_minlength":

{ "description": "ET: Minimum fiber length (in mm). This value will be used for mrTrix regardless of ET. If 999, the default from mrTrix will be used (see mrTrix documentation). DEFAULT=999", "default": 999, "type": "number" },

"ET_maxlength":

{ "description": "ET: Maximum fiber length (in mm) used in the whole brain tractrogram tracking. IMPORTANT: it requires the same amount of values as ET_angleValues. Each ET_maxlength value will be matched in position to every ET_angleValues. DEFAULT=100,150,100,150,200,150,200", "default": "100,150,100,150,200,150,200", "type": "string" },

"ET_angleValues":

{ "description": "ET: Angle cutoff values to use during ET tracking (comma-separated list). Using one value is the equivalent of not using ET. IMPORTANT: there need to be the same amount of ET_maxlength values than ET_angleValues. DEFAULT='45, 45, 25, 25, 25, 5, 5'", "default": "45, 45, 25, 25, 25, 5, 5", "type": "string" },

"ET_track_stepSizeMm":

{ "description": "ET: track stepSizeMm. DEFAULT=999", "default": 999, "type": "number"