upate with spine_generic subject

converting to 1mm isotropic and float32 images

bounding_box_dict.json

@@ -0,0 +1,21 @@
+{
+  "testing_data/sub-test001/anat/sub-test001_T1w.nii.gz":
+    [
+      7,
+      386,
+      113,
+      231,
+      1,
+      16
+    ],
+
+  "testing_data/sub-test001/anat/sub-test001_T2w.nii.gz":
+    [
+      7,
+      386,
+      113,
+      231,
+      1,
+      16
+    ]
+}

dataset_description.json

@@ -0,0 +1,6 @@
+{
+  "BIDSVersion": "1.0.1", 
+  "Name": "Spine_generic_example", 
+  "Researcher": "Julien Cohen-Adad", 
+  "Study": "Spine_generic/sub-unf01"
+}

derivatives/labels/sub-unf01/anat/sub-unf01_T2w_labels-disc-manual.json

@@ -0,0 +1 @@
+{}

derivatives/labels/sub-unf01/anat/sub-unf01_T2w_lesion-manual.nii.gz.json

@@ -0,0 +1 @@
+{}

hyperparameter_opt.json

@@ -0,0 +1,5 @@
+{
+  "training_parameters": {
+    "batch_size": [2, 4]
+  }
+}

model_config.json

@@ -0,0 +1,132 @@
+{
+  "command": "train",
+  "gpu": 7,
+  "log_directory": "testing_script",
+  "debugging": false,
+  "model_name": "unit_test",
+  "object_detection_params": {
+    "object_detection_path": null
+  },
+  "loader_parameters": {
+    "target_suffix": ["_heatmap3"],
+    "roi_suffix": null,
+    "bids_path": "testing_data/",
+    "roi_params": {
+      "suffix": null,
+      "slice_filter_roi": null
+    },
+    "contrast_params": {
+      "random_seed": 1313,
+      "training_validation": [
+        "T1w_mid"
+      ],
+      "balance": {},
+      "testing": [
+        "T1w_mid"
+      ],
+      "center_test": []
+    },
+    "slice_filter_params": {
+      "filter_empty_mask": false,
+      "filter_empty_input": true
+    },
+    "slice_axis": "sagittal",
+    "split_method": "per_patient",
+    "multichannel": false,
+    "soft_input": false
+  },
+  "split_dataset": {
+    "fname_split": null,
+    "random_seed": 1313,
+    "method": "per_patient",
+    "train_fraction": 0.66,
+    "test_fraction": 0.33,
+    "center_test": []
+  },
+  "training_parameters": {
+    "batch_size": 32,
+    "loss": {
+      "name": "DiceLoss"
+    },
+    "training_time": {
+      "num_epochs": 1,
+      "early_stopping_patience": 50,
+      "early_stopping_epsilon": 0.001
+    },
+    "scheduler": {
+      "initial_lr": 0.001,
+      "lr_scheduler": {
+        "name": "CosineAnnealingLR",
+        "base_lr": 1e-5,
+        "max_lr": 1e-2
+      }
+    },
+    "balance_samples": false,
+    "mixup_alpha": null,
+    "transfer_learning": {
+      "retrain_model": null,
+      "retrain_fraction": 1.0
+    }
+  },
+  "default_model": {
+    "name": "Unet",
+    "dropout_rate": 0.3,
+    "bn_momentum": 0.1,
+    "out_channel": 1,
+    "depth": 1
+  },
+  "FiLMedUnet": {
+    "applied": false,
+    "metadata": "contrasts",
+    "film_layers": [0, 1, 0, 0, 0, 0, 0, 0, 0, 0]
+  },
+  "missing_modality": false,
+  "attention_unet": false,
+  "mixup_bool": false,
+  "metadata": null,
+  "testing_parameters": {
+    "binarize_prediction": false,
+    "uncertainty": {
+      "epistemic": true,
+      "aleatoric": true,
+      "n_it": 2
+    }
+  },
+  "evaluation_parameters": {
+    "targetSize": {
+      "unit": "vox",
+      "thr": [
+        20,
+        100
+      ]
+    },
+    "removeSmall": {
+      "unit": "vox",
+      "thr": 3
+    },
+    "overlap": {
+      "unit": "vox",
+      "thr": 3
+    }
+  },
+  "transformation": {
+    "Resample": {
+      "wspace": 0.75,
+      "hspace": 0.75
+    },
+    "ElasticTransform": {
+      "alpha_range": [28.0, 30.0],
+      "sigma_range": [3.5, 4.5],
+      "p": 0.1
+    },
+    "RandomAffine": {
+      "degrees": 4.6,
+      "translate": [0.03, 0.03],
+      "scale": [0.98, 1]
+    },
+    "NumpyToTensor": {},
+    "NormalizeInstance": {
+      "applied_to": ["im"]
+    }
+  }
+}

model_config_test.json

@@ -0,0 +1,122 @@
+{
+  "command": "test",
+  "gpu": 0,
+  "log_directory": "testing_script",
+  "debugging": false,
+  "model_name": "model_unet_test",
+  "object_detection_params": {
+    "object_detection_path": null
+  },
+  "loader_parameters": {
+    "target_suffix": ["_lesion-manual"],
+    "roi_suffix": null,
+    "bids_path": "testing_data/",
+    "roi_params": {
+      "suffix": null,
+      "slice_filter_roi": null
+    },
+    "contrast_params": {
+      "random_seed": 1313,
+      "training_validation": [
+        "T1w"
+      ],
+      "balance": {},
+      "testing": [
+        "T1w"
+      ],
+      "center_test": []
+    },
+    "slice_filter_params": {
+      "filter_empty_mask": false,
+      "filter_empty_input": true
+    },
+    "slice_axis": "axial",
+    "split_method": "per_patient",
+    "multichannel": false,
+    "soft_input": false
+  },
+  "split_dataset": {
+    "fname_split": null,
+    "random_seed": 1313,
+    "method": "per_patient",
+    "train_fraction": 0.66,
+    "test_fraction": 0.33,
+    "center_test": []
+  },
+  "training_parameters": {
+    "batch_size": 32,
+    "loss": {
+      "name": "DiceLoss"
+    },
+    "training_time": {
+      "num_epochs": 1,
+      "early_stopping_patience": 50,
+      "early_stopping_epsilon": 0.001
+    },
+    "scheduler": {
+      "initial_lr": 0.001,
+      "lr_scheduler": {
+        "name": "CosineAnnealingLR",
+        "base_lr": 1e-5,
+        "max_lr": 1e-2
+      }
+    },
+    "balance_samples": false,
+    "mixup_alpha": null,
+    "transfer_learning": {
+      "retrain_model": null,
+      "retrain_fraction": 1.0
+    }
+  },
+  "default_model": {
+    "name": "Unet",
+    "dropout_rate": 0.3,
+    "bn_momentum": 0.1,
+    "out_channel": 1,
+    "depth": 1
+  },
+  "FiLMedUnet": {
+    "applied": false,
+    "metadata": "contrasts",
+    "film_layers": [0, 1, 0, 0, 0, 0, 0, 0, 0, 0]
+  },
+  "missing_modality": false,
+  "attention_unet": false,
+  "mixup_bool": false,
+  "metadata": null,
+  "testing_parameters": {
+    "binarize_prediction": true,
+    "uncertainty": {
+      "epistemic": true,
+      "aleatoric": true,
+      "n_it": 2
+    }
+  },
+  "evaluation_parameters": {
+    "targetSize": {
+      "unit": "vox",
+      "thr": [
+        20,
+        100
+      ]
+    },
+    "removeSmall": {
+      "unit": "vox",
+      "thr": 3
+    },
+    "overlap": {
+      "unit": "vox",
+      "thr": 3
+    }
+  },
+  "transformation": {
+    "Resample": {
+      "wspace": 0.75,
+      "hspace": 0.75
+    },
+    "NumpyToTensor": {},
+    "NormalizeInstance": {
+      "applied_to": ["im"]
+    }
+  }
+}

participants.tsv

@@ -0,0 +1,2 @@
+participant_id	sex	age	first_name	last_name	date_of_birth	date_of_scan	pathology	data_id	institution_id
+sub-unf01	unknown	-	unknown	unknown	-	unknwon	unknwon	unknown	unknown

sub-unf01/anat/sub-unf01_T1w.json

@@ -0,0 +1,64 @@
+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "Prisma_fit",
+	"InstitutionName": "IUGM",
+	"InstitutionAddress": "Chemin_Queen-Mary_4565_Montreal_District_CA_H3W_1W5",
+	"DeviceSerialNumber": "167006",
+	"StationName": "MRC35049",
+	"BodyPartExamined": "SPINE",
+	"PatientPosition": "HFS",
+	"ProcedureStepDescription": "spine_generic",
+	"SoftwareVersions": "syngo_MR_E11",
+	"MRAcquisitionType": "3D",
+	"SeriesDescription": "T1w",
+	"ProtocolName": "T1w",
+	"ScanningSequence": "GR_IR",
+	"SequenceVariant": "SK_SP_MP",
+	"ScanOptions": "IR",
+	"SequenceName": "_tfl3d1_16",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS3D", "DIS2D"],
+	"SeriesNumber": 2,
+	"AcquisitionTime": "12:33:7.032500",
+	"AcquisitionNumber": 1,
+	"SliceThickness": 1,
+	"SAR": 0.0601922,
+	"EchoTime": 0.00372,
+	"RepetitionTime": 2,
+	"InversionTime": 1,
+	"FlipAngle": 9,
+	"PartialFourier": 1,
+	"BaseResolution": 320,
+	"ShimSetting": [
+		620,
+		-7194,
+		-9127,
+		77,
+		28,
+		-20,
+		-10,
+		-23	],
+	"TxRefAmp": 266.247,
+	"PhaseResolution": 1,
+	"ReceiveCoilName": "HeadNeck_64",
+	"ReceiveCoilActiveElements": "HC1-7;NC1,2",
+	"PulseSequenceDetails": "%SiemensSeq%_tfl",
+	"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
+	"PercentPhaseFOV": 81.25,
+	"PhaseEncodingSteps": 259,
+	"AcquisitionMatrixPE": 260,
+	"ReconMatrixPE": 320,
+	"ParallelReductionFactorInPlane": 2,
+	"PixelBandwidth": 150,
+	"ImageOrientationPatientDICOM": [
+		0,
+		1,
+		0,
+		-0.00523601,
+		0,
+		-0.999986	],
+	"InPlanePhaseEncodingDirectionDICOM": "ROW",
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20180622 (JP2:OpenJPEG) GCC6.1.0"
+}