Commit 5f10c7f7 authored by Sean Fitzgibbon's avatar Sean Fitzgibbon
Browse files

yaml bugfix

parent 61b73395
{
"header": {
"title": "TIRL MBP-to-NeuN image registration routine - adapted for histology-to-histology registration",
"description": "",
"author": "Istvan N Huszar - adapted by Istvan & Amy Howard Mar 2021 - Adapted by Sean Fitz 2021"
},
"general": {
"name": "slice-to-slice",
"system": "linux",
"loglevel": "debug",
"logfile": "./logfile.log",
"paramlogfile": "./paramlog.log",
"verbose": false,
"outputdir": "./reg",
"stages": ["rotation", "rigid", "affine", "nonlinear"],
"warnings": true,
"isotropic": true
},
"moving": {
"file": "",
"storage": "mem",
"dtype": "f4",
"resolution_level": 4,
"mask": {
"file": null,
"normalise": true,
"function": null,
"automask": {
"thr": 0.00,
"uthr": 1.0
}
},
"preview": false,
"export": true,
"snapshot": true
},
"fixed": {
"file": "",
"storage": "mem",
"dtype": "f4",
"resolution_level": 4,
"mask": {
"file": null,
"normalise": true,
"function": null,
"automask": {
"thr": 0.0,
"uthr": 1.0
}
},
"preview": false,
"export": false,
"snapshot": true
},
"preprocessing": {
"moving": ["moving_preprocessing", "match_fixed_resolution"],
"fixed": ["fixed_preprocessing"]
},
"regparams": {
"init": {
"scale": {
"x0": 1.0,
"lb": 0.95,
"ub": 1.05
},
"rotation": {
"x0": 0.0,
"mode": "deg",
"lb": -10,
"ub": 10
},
"translation": {
"x0": [0.0, 0.0],
"lb": [-5.0, -5.0],
"ub": [5.0, 5.0]
},
"affine": {
"x0": [1.0, 0.0, 0.0, 0.0, 1.0, 0.0],
"lb": [0.95, -0.2, -1.0, -0.2, 0.95, -1.0],
"ub": [1.05, 0.2, 1.0, 0.2, 1.05, 1.0]
},
"nonlinear": {
"x0": 0.0,
"lb": null,
"ub": null
}
},
"rotsearch": {
"coarse": 1,
"scale": 0.125,
"visualise": false,
"xtol_rel": 0.01,
"xtol_abs": [0.001, 0.001, 0.001, 0.001],
"opt_step": 0.5
},
"rigid": {
"scaling": [160, 80, 40, 20, 10, 5],
"smoothing": [0, 0, 0, 0, 0],
"xtol_rel": 0.01,
"xtol_abs": [0.001, 0.001, 0.001, 0.001],
"opt_step": 0.1,
"visualise": false
},
"affine": {
"scaling": [160, 80, 40, 20, 10, 5],
"smoothing": [0, 0, 0],
"xtol_rel": 0.01,
"xtol_abs": [0.001, 0.001, 0.001, 0.001, 0.001, 0.001],
"opt_step": 0.1,
"visualise": false
},
"nonlinear": {
"scaling1": [8, 4, 2, 1],
"scaling": [160, 80, 40, 20, 10, 5],
"smoothing": [0, 0, 0, 0, 0, 0],
"sigma": 1,
"truncate": 1.5,
"regweight": 0.4,
"regweight1": 0.6,
"maxiter": [20, 20, 20, 20, 10, 5],
"xtol_abs": 0.1,
"xtol_rel": 0.01,
"visualise": false
}
}
}
......@@ -106,7 +106,7 @@ regparams:
scaling: [160, 80, 40, 20, 10, 5]
smoothing: [0, 0, 0]
visualise: false
xtol_abs: [0.001, 0.001, 0.001, 0.001]
xtol_abs: [0.001, 0.001, 0.001, 0.001, 0.001, 0.001]
xtol_rel: 0.01
nonlinear:
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment