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Commit e6988a71 authored by Istvan N Huszar's avatar Istvan N Huszar
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Partial bugfix for TIRLFile object ID redundancy problem.

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share/example/config/2_block_to_slice.json 0 → 100644
View file @ e6988a71
{
"header": {
"title": "TIRL MND (Stage 2) Block-to-slice image registration routine",
"description": "Developed for the Oxford MND Post-Mortem Imaging Biomarkers study.",
"author": "Istvan N Huszar"
},
"general": {
"name": "block_to_slice",
"direction": "b2s",
"system": "linux",
"loglevel": "debug",
"logfile": "/Users/inhuszar/temp/stage2/logfile.log",
"paramlogfile": "/Users/inhuszar/temp/stage2/paramlog.log",
"verbose": false,
"outputdir": "/Users/inhuszar/temp/stage2",
"stages": ["rigid", "affine", "nonlinear"],
"warnings": false,
"cost": "MIND"
},
"block": {
"file": "/Users/inhuszar/temp/2_tissue_block/tissue_block.tif",
"storage": "mem",
"dtype": "f4",
"resolution": 0.05,
"mask": {
"file": null,
"normalise": true,
"function": null,
"automask": {
"thr": 0.1,
"uthr": 1.0
}
},
"preview": false,
"export": true,
"snapshot": true
},
"slice": {
"file": "/Users/inhuszar/temp/3_brain_slice/0.tif",
"storage": "mem",
"dtype": "f4",
"resolution": 0.05,
"mask": {
"file": null,
"normalise": true,
"function": null,
"automask": {
"thr": 0.1,
"uthr": 1
}
},
"preview": false,
"export": false,
"snapshot": false
},
"preprocessing": {
"block": ["block_preprocessing"],
"slice": ["slice_preprocessing"]
},
"regparams": {
"init": {
"scale": {
"x0": [1.0, 1.0],
"lb": [0.9, 0.9],
"ub": [1.1, 1.1]
},
"rotation": {
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"mode": "deg",
"lb": -180,
"ub": 180
},
"translation": {
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"lb": [-5.0, -5.0],
"ub": [5.0, 5.0]
},
"affine": {
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"lb": [0.8, -1.0, -5.0, -1.0, 0.8, -5.0],
"ub": [1.2, 1.0, 5.0, 1.0, 1.2, 5.0]
},
"nonlinear": {
"x0": 0.0,
"lb": null,
"ub": null
}
},
"sites": "/Users/inhuszar/temp/3_brain_slice/sites/sites.txt",
"jiggle": {
"scale": 0.1,
"xrange": [10.0, 10.0],
"xstops": [3, 3],
"rotsteps": 12,
"xtol_abs": [0.01, 0.1, 0.1],
"xtol_rel": 0.001,
"opt_step": [0.025, 1.0, 1.0],
"n_best": 3,
"visualise": false
},
"rigid": {
"scaling": [10, 5],
"smoothing": [0, 0],
"xtol_rel": 0.001,
"xtol_abs": [0.001, 0.001, 0.001, 0.05, 0.05],
"opt_step": [0.025, 0.1, 0.1, 1.0, 1.0],
"visualise": false
},
"affine": {
"scaling": [5, 2, 1],
"smoothing": [0, 0, 0, 0],
"xtol_rel": 0.001,
"xtol_abs": [0.001, 0.001, 0.01, 0.001, 0.001, 0.01],
"opt_step": [0.05, 0.05, 1.0, 0.05, 0.05, 1.0],
"visualise": false
},
"nonlinear": {
"scaling": [20, 10, 5],
"smoothing": [0, 0, 0],
"sigma": 1,
"truncate": 1.5,
"regweight": 0.3,
"maxiter": [20, 20, 20],
"xtol_abs": 0.1,
"xtol_rel": 0.01,
"visualise": false
}
}
}
share/example/config/3_slice_to_volume.json 0 → 100644
View file @ e6988a71
{
"header": {
"title": "TIRL MND (Stage 3) Unified slice-to-volume image registration routine",
"description": "Developed for the Oxford MND Post-Mortem Imaging Biomarkers study.",
"author": "Istvan N Huszar"
},
"general": {
"name": "mnd.coronal",
"system": "linux",
"loglevel": "debug",
"logfile": null,
"paramlogfile": "/Users/inhuszar/temp/stage3/paramlogs.log",
"verbose": false,
"outputdir": "/Users/inhuszar/temp/stage3",
"stages": [1, 2, 3, 4, 5, 3, 4, 5],
"isotropic": true,
"cost": "MIND",
"warnings": false
},
"slice": {
"file": "/Users/inhuszar/temp/3_brain_slice/0.tif",
"storage": "mem",
"dtype": "f4",
"resolution": 0.05,
"mask": {
"file": null,
"normalise": true,
"function": null,
"automask": {
"thr": 0.1,
"uthr": 1.0
}
},
"preview": false,
"export": true,
"snapshot": true
},
"volume": {
"file": "/Users/inhuszar/temp/4_mri/mri.nii.gz",
"storage": "mem",
"dtype": "f4",
"resolution": null,
"usesqform": true,
"mask": {
"file": null,
"normalise": true,
"function": null,
"automask": {
"thr": 0.0,
"uthr": 1.0
}
},
"preview": false,
"export": true
},
"preprocessing": {
"slice": ["slice_preprocessing", "match_volume_resolution"],
"volume": ["volume_preprocessing"]
},
"regparams": {
"init": {
"scale2d": 1.0,
"rot2d": -90,
"trans2d": [0, 0],
"rot3d": [0, 0, 0],
"affine3d": [1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0],
"trans3d": [0, 0, 0]
},
"stage_1": {
"export": {
"timage": true,
"snapshot": true,
"target_mask": true,
"source_mask": false
},
"visualise": false,
"cleanup": true,
"slab": {
"centre": [2.2, 66.99, -6.3],
"normal": [0, 1, 0],
"offset": 0,
"thickness": 10,
"n_positions": 5,
"range": [0, 10, 10],
"n_orientations": [1, 3, 3]
},
"iterations": 1,
"n_cpu": -1,
"top": 0.3,
"slice_scaling": [2, 1],
"slice_smoothing": [0, 0],
"volume_scaling": [2, 1],
"volume_smoothing": [0, 0],
"constrained": true,
"try_unconstrained": false,
"opt_step": 0.1,
"stage_1a": {
"scale2d_lower_delta": 0.05,
"scale2d_upper_delta": 0.05,
"rot2d_lower_delta": 20.0,
"rot2d_upper_delta": 20.0,
"trans2d_lower_delta": [10.0, 10.0],
"trans2d_upper_delta": [10.0, 10.0],
"xtol_abs": [0.01, 0.01, 0.01, 0.01]
},
"stage_1b": {
"scale2d_lower_delta" : 0.05,
"scale2d_upper_delta" : 0.05,
"rot3d_lower_delta" : [5.0, 10.0, 10.0],
"rot3d_upper_delta" : [5.0, 10.0, 10.0],
"trans3d_lower_delta" : [3.0, 3.0, 3.0],
"trans3d_upper_delta" : [3.0, 3.0, 3.0],
"xtol_abs": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01]
}
},
"stage_2": {
"export": {
"timage": true,
"snapshot": true,
"costmap": true,
"target_mask": true,
"source_mask": false
},
"visualise": false,
"slice_scaling": [1],
"volume_scaling": [1],
"slice_smoothing": [0],
"volume_smoothing": [0],
"lower_delta": [0.1, 0.1, 0.1, 1.0, 0.1, 0.1, 0.1, 1.0, 0.1, 0.1, 0.1, 1.0],
"upper_delta": [0.1, 0.1, 0.1, 1.0, 0.1, 0.1, 0.1, 1.0, 0.1, 0.1, 0.1, 1.0],
"xtol_rel": 0.01,
"opt_step": 0.1
},
"stage_3": {
"export": {
"timage": true,
"snapshot": true,
"control_points": true,
"target_mask": true,
"source_mask": false
},
"visualise": false,
"support": {
"mode": "km",
"points": 16,
"mask": {
"file": null,
"normalise": true,
"automask": {
"thr": 0.01,
"uthr": 1
}
}
},
"optsize": 4,
"vectorder": "xy",
"slice_scaling": [1],
"slice_smoothing": [0],
"volume_scaling": [1],
"volume_smoothing": [0],
"lower_dxy": 5.0,
"upper_dxy": 5.0,
"regweight": 0,
"model": "multiquadric",
"opt_step": 0.1,
"xtol_abs": 0.01
},
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"export": {
"timage": true,
"snapshot": true,
"control_points": true,
"target_mask": true,
"source_mask": false
},
"visualise": false,
"support": {
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"points": 16,
"mask": {
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"normalise": true,
"function": null,
"automask": {
"thr": 0.01,
"uthr": 1
}
}
},
"optsize": 4,
"vectorder": "xyz",
"slice_scaling": [1],
"slice_smoothing": [0],
"volume_scaling": [1],
"volume_smoothing": [0],
"lower_dxy": 3.0,
"lower_dz": 3.0,
"upper_dxy": 3.0,
"upper_dz": 3.0,
"regweight": 0,
"model": "multiquadric",
"opt_step": 0.1,
"xtol_abs": 0.01
},
"stage_5": {
"export": {
"timage": true,
"snapshot": true,
"target_mask": true,
"source_mask": false
},
"visualise": false,
"mask": {
"file": null,
"normalise": true,
"function": null,
"automask": {
"thr": 0.01,
"uthr": 1.0
}
}
}
}
}
share/example/example_reg_commands.sh 0 → 100644
View file @ e6988a71
#!/bin/sh
# Runs the example registration pipeline
EXAMPLE="."
tirl histology_to_block --config ${EXAMPLE}/config/1_histology_to_block.json --verbose
tirl find_sites ${EXAMPLE}/3_brain_slice/*.tif --verbose
tirl block_to_slice --config ${EXAMPLE}/config/2_block_to_slice.json --verbose
tirl slice_to_volume --config ${EXAMPLE}/config/3_slice_to_volume.json --verbose
tirl combine --histo ${EXAMPLE}/stage1/fixed4_nonlinear.timg --block ${EXAMPLE}/stage2/fixed4_nonlinear.timg --slice ${EXAMPLE}/stage3/4_stage4.timg --vol ${EXAMPLE}/stage3/volume.timg --out ${EXAMPLE}/combined
share/logo/logo.svg 0 → 100755
View file @ e6988a71
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share/resources/fsl/T1_to_MNI_lin.mat 0 → 100755
View file @ e6988a71
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