Parameters¶
Adding -params¶
Definition of the sequence of nodes in processing pipelines, as well as general parameters, are specified by json file. When specifying a -species and -soft (see Commands), the corresponding default parameter file will be used; They are located in the workflows directory of the package.
The original parameter file can be altered by some options in -soft (e.g. _robustreg, _prep, etc.; see Commands).
Here is an example of the params.json with parameters -soft ANTS_skull for -species macaque:
{
"general":
{
"template_name": "NMT_v2.0_asym"
},
"short_preparation_pipe":
{
"aladin_T2_on_T1":{},
"crop_aladin_pipe":
{
"reg_T1_on_template":
{
"rig_only_flag" : true
},
"reg_T1_on_template2":
{
"rig_only_flag":true
}
},
"pad_template":
{
"operation" : "PadImage",
"op2" : "70"
},
"denoise":
{
"shrink_factor": 2
},
"N4debias":
{
"dimension": 3,
"bspline_fitting_distance": 200,
"n_iterations": [50, 50, 40, 30],
"convergence_threshold": 1e-08,
"shrink_factor": 2,
"args": "-r 0 --verbose 1"
}
},
"extract_pipe":
{
"atlas_brex":
{
"f": 0.5,
"reg": 1,
"wrp": "10,10,10",
"msk": "a,0,0",
"dil": 2,
"nrm": 1
}
},
"debias":
{
"s": 2
},
"brain_segment_pipe":
{
"reg":
{
"n": 2,
"m": "ref",
"dof": 12
},
"segment_atropos_pipe":
{
"use_priors": 0.0,
"Atropos":
{
"dimension": 3
},
"tissue_dict":
{
"gm": [2, 3],
"wm": 4,
"csf": [1, 5]
}
}
},
"export_5tt_pipe": {},
"IsoSurface_brain_pipe":
{
"merge_brain_tissues":
{
"keep_indexes": [2, 3, 4]
}
},
"IsoSurface_tissues_pipe":
{
},
"skull_t1_pipe":
{
"headmask_t1_pipe":
{
"t1_head_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 9.0
},
"t1_head_erode":
{
"kernel_shape": "boxv",
"kernel_size": 9.0
}
},
"skullmask_t1_pipe":
{
"t1_fast":
{
"args": "-l 10",
"img_type": 1,
"output_biascorrected": true,
"output_biasfield": true
},
"t1_head_erode_skin":
{
"kernel_shape": "boxv",
"kernel_size": 9.0
},
"t1_skull_gcc_erode":
{
"kernel_shape": "boxv",
"kernel_size": 6.0
},
"t1_skull_gcc_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 6.0
},
"t1_skull_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 4.0
},
"t1_skull_erode":
{
"kernel_shape": "boxv",
"kernel_size": 4.0
},
"t1_skull_fov":
{
"brainsize": 45
}
}
},
"skull_petra_pipe":
{
"headmask_petra_pipe":
{
"petra_head_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 7.0
},
"petra_head_erode":
{
"kernel_shape": "boxv",
"kernel_size": 7.0
}
},
"skullmask_petra_pipe":
{
"petra_fast":
{
"args": " -l 10",
"img_type": 3,
"output_biascorrected": true,
"output_biasfield": true
},
"petra_head_erode_skin":
{
"kernel_shape": "boxv",
"kernel_size": 9.0
},
"petra_skull_gcc_erode":
{
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"petra_skull_gcc_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"petra_skull_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 7.0
},
"petra_skull_erode":
{
"kernel_shape": "boxv",
"kernel_size": 7.0
},
"petra_skull_fov":
{
"brainsize": 45
}
}
},
"skull_ct_pipe":
{
"align_ct_on_T1_2":
{
},
"skullmask_ct_pipe":
{
"ct_skull_auto_mask":
{
"kmeans": true,
"sample_bins": 30,
"distance": 10,
"operation": "lower",
"index": 2
},
"ct_skull_dilate":
{
"operation" : "modal",
"kernel_shape" : "boxv",
"kernel_size" : 3.0
},
"ct_skull_erode":
{
"kernel_shape" : "boxv",
"kernel_size" : 3.0
},
"ct_skull_fov":
{
"brainsize" : 45
}
}
},
"angio_pipe":
{
"angio_denoise":
{
"shrink_factor": 1
},
"angio_fast":
{
"args": " -l 10",
"img_type": 3,
"output_biascorrected": true,
"output_biasfield": true
}
}
}
It is also possible to alter values of some nodes for individual sessions/subjects. See individual parameter section).
Note: Individual parameter will not modify the pipeline sequence itself, a value specified in indiv_params for a node that do not exists in params will ignored
Advanced parameters settings¶
For advanced user, it is however possible to pass the pipeline sequence as a params.json file. In this case all further alteration will be canceled.
Here is json file with all possible nodes to be tuned; Some node are optional, some nodes are exclusive with each other (XOR). All parameters given here are give as examples and may vary
{
"skull_t1_pipe":
{
"comment": "will be removed if option _noheadmask or _noskullmask is provided in -soft)",
"headmask_t1_pipe":
{
"comment": "the following nodes are mutually exclusive, but are mandatory if headmask_t1_pipe is defined",
"t1_head_li_mask":
{
"comment": "DEFAULT (do not need to be specied in params)",
"params": "Uses threshold_li from skimage.filters (from macapype, also used in remove_capsule_pipe)",
"comment": "No argument"
},
"comment": "OR",
"t1_head_mask_thr":
{
"comment": "OPTIONAL",
"params": "Threshold (FSL)",
"thr": "300"
},
"comment": "OR",
"t1_head_auto_mask":
{
"comment": "OPTIONAL",
"params": "mask_auto_img (python)",
"kmeans": true,
"operation": "lower",
"index": 2
},
"comment": "The following 2 nodes are OPTIONAL either have to be both defined or none of them",
"comment": "allows to cut some elements before gcc is applied",
"comment": "are used in -soft _skullnoisypetra",
"t1_head_gcc_erode":
{
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"t1_head_gcc_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"t1_head_dilate":
{
"params": "DilateImage (FSL)",
"operation" : "modal",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
},
"t1_head_erode":
{
"params": "ErodeImage (FSL)",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
}
},
"comment": "will be removed if option _noskullmask is provided in -soft)",
"skullmask_t1_pipe":
{
"t1_fast":
{
"params": "FAST (FSL)",
},
"comment": "The following 2 nodes are OPTIONAL and mutually exclusive",
"comment": "If not defined fast pve_0 is used as mask for skull",
"t1_skull_auto_mask":
{
"comment": "OPTIONAL",
"params": "mask_auto_img (python)",
"kmeans": true,
"operation": "lower",
"index": 2
},
"comment": "OR",
"t1_skull_mask_thr":
{
"comment": "OPTIONAL",
"params": "Threshold (FSL)",
"thr": "300"
},
"t1_head_erode_skin":
{
"comment": "OPTIONAL",
"params": "ErodeImage (FSL)",
"kernel_shape" : "boxv",
"kernel_size" : 14.0
},
"comment": "The following 2 nodes are OPTIONAL either have to be both defined or none of them",
"comment": "allows to cut some elements before gcc is applied",
"comment": "are used in -soft _skullnoisypetra",
"t1_skull_gcc_erode":
{
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"t1_skull_gcc_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"t1_skull_dilate":
{
"params": "DilateImage (FSL)",
"operation" : "modal",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
},
"t1_skull_erode":
{
"params": "ErodeImage (FSL)",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
},
"t1_skull_fov":
{
"comment": "OPTIONAL",
"params": "RobustFOV (FSL)",
"brainsize" : "45",
}
},
},
"skull_ct_pipe":
{
"align_ct_on_T1_2":
{
"comment": "OPTIONAL",
"comment": "Cannot be modified",
"params": "RegAladin (NiftyReg)"
},
"comment": "will be removed if option _noheadmask or _noskullmask is provided in -soft)",
"skullmask_ct_pipe":
{
"comment": "the following nodes are mutually exclusive, but are mandatory if skullmask_ct_pipe is defined ",
"ct_head_mask_thr":
{
"params": "Threshold (FSL)",
"thr": "300"
},
"comment": "OR",
"ct_head_auto_mask":
{
"params": "mask_auto_img (python)",
"kmeans": true,
"operation": "lower",
"index": 2
},
"ct_skull_dilate":
{
"params": "DilateImage (FSL)",
"operation" : "modal",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
},
"ct_skull_erode":
{
"params": "ErodeImage (FSL)",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
}
},
"skull_petra_pipe":
{
"avg_reorient_pipe":
{
"comment": "OPTIONAL",
"params": "see corresponding doc in short_preparation_pipe in macapype"
},
"comment": "will be removed if option _noheadmask or _noskullmask is provided in -soft)",
"headmask_petra_pipe":
{
"petra_itk_debias":
{
"comment": "OPTIONAL",
"params": "SimpleITK N4BiasFieldCorrectionImageFilter dirty wrap (defined in macapype.nodes.correc_bias)",
"comment": "TODO: Should be made a proper nipype node",
},
"comment": "the following nodes are mutually exclusive, but are mandatory if headmask_t1_pipe is defined",
"petra_head_li_mask":
{
"comment": "DEFAULT (do not need to be specied in params)",
"params": "Uses threshold_li from skimage.filters (from macapype, also used in remove_capsule_pipe)",
"comment": "No argument"
},
"comment": "OR",
"petra_head_mask_thr":
{
"params": "Threshold (FSL)",
"thr": "300"
},
"comment": "OR",
"petra_head_auto_mask":
{
"params": "mask_auto_img (python)",
"kmeans": true,
"operation": "lower",
"index": 2
},
"comment": "The following 2 nodes are OPTIONAL either have to be both defined or none of them",
"comment": "allows to cut some elements before gcc is applied",
"comment": "are used in -soft _skullnoisypetra",
"petra_head_gcc_erode":
{
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"petra_head_gcc_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"petra_head_dilate":
{
"params": "DilateImage (FSL)",
"operation" : "modal",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
},
"petra_head_erode":
{
"params": "ErodeImage (FSL)",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
}
},
"comment": "will be removed if option _noskullmask is provided in -soft)",
"skullmask_petra_pipe":
{
"petra_fast":
{
"params": "FAST (FSL)",
},
"comment": "The following 2 nodes are OPTIONAL and mutually exclusive",
"comment": "If not defined fast pve_0 is used as mask for skull",
"petra_skull_auto_mask":
{
"comment": "OPTIONAL",
"params": "mask_auto_img (python)",
"kmeans": true,
"operation": "lower",
"index": 2
},
"comment": "OR",
"petra_skull_mask_thr":
{
"comment": "OPTIONAL",
"params": "Threshold (FSL)",
"thr": "300"
},
"comment": "The following 2 nodes are OPTIONAL either have to be both defined or none of them",
"comment": "allows to cut some elements before gcc is applied",
"comment": "are used in -soft _skullnoisypetra",
"petra_skull_gcc_erode":
{
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"petra_skull_gcc_dilate":
{
"operation": "modal",
"kernel_shape": "boxv",
"kernel_size": 3.0
},
"petra_head_erode_skin":
{
"comment": "OPTIONAL",
"params": "ErodeImage (FSL)",
"kernel_shape" : "boxv",
"kernel_size" : 14.0
},
"petra_skull_dilate":
{
"params": "DilateImage (FSL)",
"operation" : "modal",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
},
"petra_skull_erode":
{
"params": "ErodeImage (FSL)",
"kernel_shape" : "boxv",
"kernel_size" : 13.0
},
"petra_skull_fov":
{
"comment": "OPTIONAL",
"params": "RobustFOV (FSL)",
"brainsize" : "45",
},
},
"comment": "Still optional, should be used with caution",
"angio_pipe":
{
"angio_mask_thr":
{
"params": "Threshold (FSL)",
"thr": "300"
},
"comment": "OR",
"angio_auto_mask":
{
"params": "FAST (FSL)"
}
}
}
Note: The json file provided here only pass the node available in pipelines specific to skullTo3d processing. A functional pipeline will also require some pipeline sequence from macapype itself, a minima the definition of a short_preparation_pipe sequence of nodes. See macapype params page for more details.