Individual Parameters

Adding -indiv

You can include “-indiv indiv_params.json” in the python command, for specifiying parameters specific parameters:

$ python workflows/segment_petra.py -data ~/Data_maca -out ./local_test -soft SPM -params params.json -indiv indiv_params.json

Advanced parameters settings

Here is json file with all possible nodes to be tuned in indiv_params; In particular, the specifications of sub- and ses- are mandatory before the specification of nodes; Also note that the nodes are specified directly, without specifiying the sub-pipelines they belong to.

The nodes belonging to “short_data_preparation” pipeline (see `Params<params>`_) are common to both -soft ANTS and SPM :

{
    "sub-test":
    {
        "ses-01":
        {
            "reorient":
            {
                "comment": "OPTIONAL node in params",
                "params": "SwapDimensions (FSL)",
                "new_dims": "x z -y"
            },

            "crop_T1":
            {
                "comment": "OPTIONAL node in params",
                "params": "fslroi (FSL)",
                "args": 0.8
            },

            "reg_T1_on_template":
            {
                "params": "RegAladin (NiftyReg)"

            },
            "reg_T1_on_template2":
            {
                "comment": "OPTIONAL node in params",
                "comment": "typically used with -soft _robustreg ",

                "params": "RegAladin (NiftyReg)"

            }
        }
    }
}

For -soft SPM, here is the set of nodes that can be individually tuned:

{
    "sub-test":
    {
        "ses-01":
        {
            "debias":
            {
                "params": "T1xT2BiasFieldCorrection (local wrap of Regis Trapeau tools)",

                "s": 2
            },

            "reg":
            {
                "params": "IterREGBET (local wrap of Regis Trapeau tools)",

                "n": 2,
                "m": "ref",
                "dof": 12
            },


            "threshold_gm":
            {
                "params": "Threshold (FSL)",

                "thr": 0.5
            },
            "threshold_wm":
            {
                "params": "Threshold (FSL)",

                "thr": 0.5
            },
            "threshold_csf":
            {
                "params": "Threshold (FSL)",

                "thr": 0.5
            }
        }
    }
}

For -soft ANTS, here is the set of nodes that can be individually tuned:

{
    "sub-test":
    {
        "ses-01":
        {
            "N4debias":
            {
                "params": "N4BiasFieldCorrection (ANTS)",
                "comment": "OPTIONAL",

                "dimension": 3,
                "bspline_fitting_distance": 200,
                "n_iterations": [50, 50, 40, 30],
                "convergence_threshold": 0.00000001,
                "shrink_factor": 2,
                "args": "-r 0 --verbose 1"
            },
            "comment": "OR",
            "fast":
            {
                "comment": "OPTIONAL",
                "params": "FAST (FSL)",
            },

            "atlas_brex":
            {
                "f": 0.8
            },

            "debias":
            {
                "comment": "OPTIONAL",
                "params": "T1xT2BiasFieldCorrection (local wrap of Regis Trapeau tools)",
                "commnet": "# TODO is not used now... in code" ,
                "s": 2
            },



            "norm_intensity":
            {
                "comment": "OPTIONAL node in params, if register_NMT_pipe is defined",
                "params": "N4BiasFieldCorrection (ANTS)"
            },
            "comment": "OR",
            "reg":
            {
                "comment": "OPTIONAL node in params, if reg is defined",
                "params": "IterREGBET (local wrap of Regis Trapeau tools)",

                "n": 2,
                "m": "ref",
                "dof": 12
            }
        }
    }
}