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, as for macapype individual paramters, the nodes are specified directly, without specifiying the sub-pipelines they belong to.

Please refer to the parameter page for more explanation on the possible structure of nodes.

{
    "sub-test":
    {
        "ses-01":
        {
            "comment": "corresponds to skull_t1_pipe (skull_pipe.py)",

            "t1_head_mask_thr":
            {
                "thr": "300"

            },
            "comment": "OR",
            "t1_head_auto_mask":
            {
                "kmeans": true,
                "operation": "lower",
                "index": 2
            },

            "t1_head_dilate":
            {
                "operation" : "modal",
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },
            "t1_head_erode":
            {
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },

            "t1_debias":
            {
                "comment": "if t1_debias is defined in params"
            },

            "t1_fast":
            {
            },


            "t1_skull_auto_mask":
            {
                "comment": "if t1_skull_auto_mask is defined in params",

                "kmeans": true,
                "operation": "lower",
                "index": 2
            },
            "comment": "OR",
            "t1_skull_mask_thr":
            {
                "comment": "if t1_skull_mask_thr is defined in params",
                "thr": "300"

            },

            "t1_head_erode_skin":
            {

                "comment": "if t1_head_erode_skin is defined in params",

                "kernel_shape" : "boxv",
                "kernel_size" : 14.0
            },
            "t1_skull_dilate":
            {
                "operation" : "modal",
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },
            "t1_skull_erode":
            {
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },
            "t1_skull_fov":
            {
                "comment": "if t1_skull_fov is defined in params",

                "brainsize": 45
            },


            "comment": "corresponds to skull_ct_pipe (skull_pipe.py)",

            "ct_head_mask_thr":
            {
                "thr": "300"

            },
            "comment": "OR",
            "ct_head_auto_mask":
            {
                "kmeans": true,
                "operation": "lower",
                "index": 2
            },

            "ct_skull_dilate":
            {
                "operation" : "modal",
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },
            "ct_skull_erode":
            {
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },

            "ct_skull_fov":
            {
                "comment": "if ct_skull_fov is defined in params",

                "brainsize": 45
            },


            "comment": "corresponds to skull_petra_pipe (skull_pipe.py)",

            "avg_reorient_pipe":
            {

                "comment": "if avg_reorient_pipe is defined in params",

            },

            "petra_head_mask_thr":
            {
                "thr": "300"

            },
            "comment": "OR",
            "petra_head_auto_mask":
            {
                "kmeans": true,
                "operation": "lower",
                "index": 2
            },


            "petra_head_dilate":
            {
                "operation" : "modal",
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },
            "petra_head_erode":
            {
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },

            "petra_debias":
            {
                "comment": "if petra_debias is defined in params"
            },

            "petra_fast":
            {
            },


            "petra_skull_auto_mask":
            {
                "comment": "if petra_skull_auto_mask is defined in params",

                "kmeans": true,
                "operation": "lower",
                "index": 2
            },
            "comment": "OR",
            "petra_skull_mask_thr":
            {
                "comment": "if petra_skull_mask_thr is defined in params",
                "thr": "300"

            },

            "petra_head_erode_skin":
            {

                "comment": "if petra_head_erode_skin is defined in params",

                "kernel_shape" : "boxv",
                "kernel_size" : 14.0
            },


            "petra_skull_dilate":
            {
                "operation" : "modal",
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },
            "petra_skull_erode":
            {
                "kernel_shape" : "boxv",
                "kernel_size" : 13.0
            },

            "petra_skull_fov":
            {
                "comment": "if petra_skull_fov is defined in params",

                "brainsize": 45
            },


            "comment": "corresponds to angio_pipe (angio_pipe.py)",

            "angio_mask_thr":
            {
                "thr": "300"

            },
            "comment": "OR",
            "angio_auto_mask":
            {
                "params": "FAST (FSL)"
            }
        }
    }
}