Parameters

All the params spefications are in each function of the API, as well the spefications available for Individual Parameters.

N.B. in the newest version of macapype, the -params can be replaced the option -species followed by the NHP species corresponding to the image, e.g. {macaque | marmo | baboon | chimp}, and a default parameter, tested for this species, will be used. It is however still possible to use the -params option and provide a params.json for advanced users

Here is an example of the params.json corresponding to segment_pnh_spm_based pipeline for macaque:

{
    "general":
    {
        "template_name": "inia19"
    },
    "short_preparation_pipe":
    {
        "crop_T1":
        {
            "args": "should be defined in indiv"
        }
    },
    "debias":
    {
        "s": 4
    },
    "reg":
    {
        "n": 2,
        "m": "ref",
        "dof": 12
    },
    "old_segment_pipe":
    {
        "segment":
        {
            "gm_output_type": [false, false, true],
            "wm_output_type": [false, false, true],
            "csf_output_type": [false, false, true]
        },
        "threshold_gm":
        {
            "thresh": 0.5
        },
        "threshold_wm":
        {
            "thresh": 0.5
        },
        "threshold_csf":
        {
            "thresh": 0.5
        }
    },
    "mask_from_seg_pipe":
    {
        "dilate_mask":
        {
            "kernel_shape": "sphere",
            "kernel_size": 2
        },
        "erode_mask":
        {
            "kernel_shape": "sphere",
            "kernel_size": 2
        }
    },
    "regex_subs":
    {
        "FLAIR_flirt": "preproc-coreg_FLAIR"
    }
}