From fda5b8b85a438574d1952b497c48ceb72d649663 Mon Sep 17 00:00:00 2001 From: AndrewBeers Date: Fri, 27 Oct 2017 17:57:37 -0400 Subject: [PATCH 1/4] feat: First draft, glioblastoma JSON --- QTIM_Glioblastoma.json | 81 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 QTIM_Glioblastoma.json diff --git a/QTIM_Glioblastoma.json b/QTIM_Glioblastoma.json new file mode 100644 index 0000000..c35cea6 --- /dev/null +++ b/QTIM_Glioblastoma.json @@ -0,0 +1,81 @@ +{ + "name": "Glioblastoma Segmenter", + "number_of_inputs": 4, + "task": "Segmentation.", + "organ": "Brain", + "modality": "MRI", + "train_test_data_details": "The model is trained on pre-processed brain MRIs from the BRATS2017 competition.", + "briefdescription": "Segmentation of glioblastoma into whole tumor (peritumoral edema and necrosis) and enhancing tumor.", + "detaileddescription": "", + "website": "", + "citation": "", + "version": "0.1", + "docker": { + "dockerhub_repository": "qtimlab/deepinfer_glioblastoma", + "digest": "", + "size": "6.77 GB" + }, + "model_name": "qtim_glioblastoma", + "data_path": "/INPUT_DATA", + "members": [ + { + "name": "T2", + "type": "volume", + "iotype": "input", + "voltype": "ScalarVolume", + "detaileddescriptionSet": "T2-weighted MRI volume.\n", + "default": "std::vector(3, 64)", + "itk_type": "typename FilterType::SizeType" + }, + { + "name": "T1", + "type": "volume", + "iotype": "input", + "voltype": "ScalarVolume", + "detaileddescriptionSet": "T1-weighted MRI volume.\n", + "default": "std::vector(3, 64)", + "itk_type": "typename FilterType::SizeType" + }, + { + "name": "T1POST", + "type": "volume", + "iotype": "input", + "voltype": "ScalarVolume", + "detaileddescriptionSet": "T1-weighted MRI post-contrast volume.\n", + "default": "std::vector(3, 64)", + "itk_type": "typename FilterType::SizeType" + }, + { + "name": "FLAIR", + "type": "volume", + "iotype": "input", + "voltype": "ScalarVolume", + "detaileddescriptionSet": "FLAIR MRI volume.\n", + "default": "std::vector(3, 64)", + "itk_type": "typename FilterType::SizeType" + }, + { + "name": "BiasCorrection", + "type": "bool", + "default": "true", + "detaileddescriptionSet": "Apply N4BiasCorrection before segmentation.\n", + "iotype": "parameter" + }, + { + "name": "Preprocess", + "type": "bool", + "default": "true", + "detaileddescriptionSet": "Co register and resample images to isotropic space before segmentation.\n", + "iotype": "parameter" + }, + { + "name": "Output", + "type": "volume", + "iotype": "output", + "voltype": "LabelMap", + "detaileddescriptionSet": "Output labelmap for the segmentation results.\n", + "default": "std::vector(3, 64)", + "itk_type": "typename FilterType::SizeType" + } + ] +} \ No newline at end of file From 7c32677ae71df41bf9096ba72aa016811eb1fa00 Mon Sep 17 00:00:00 2001 From: Andrew Beers Date: Mon, 8 Jan 2018 12:55:36 -0500 Subject: [PATCH 2/4] Update qtim_glioblastoma to DeepNeuro --- ...astoma.json => DeepNeuro_Glioblastoma.json | 29 ++++++++++++------- 1 file changed, 18 insertions(+), 11 deletions(-) rename QTIM_Glioblastoma.json => DeepNeuro_Glioblastoma.json (72%) diff --git a/QTIM_Glioblastoma.json b/DeepNeuro_Glioblastoma.json similarity index 72% rename from QTIM_Glioblastoma.json rename to DeepNeuro_Glioblastoma.json index c35cea6..7dbfb9b 100644 --- a/QTIM_Glioblastoma.json +++ b/DeepNeuro_Glioblastoma.json @@ -1,21 +1,21 @@ { - "name": "Glioblastoma Segmenter", + "name": "DeepNeuro_Glioblastoma", "number_of_inputs": 4, - "task": "Segmentation.", + "task": "Segmentation", "organ": "Brain", "modality": "MRI", - "train_test_data_details": "The model is trained on pre-processed brain MRIs from the BRATS2017 competition.", + "train_test_data_details": "The model is trained on pre-processed brain MRIs from the BRATS2017 competition, as well as private datasets from multiple instituions.", "briefdescription": "Segmentation of glioblastoma into whole tumor (peritumoral edema and necrosis) and enhancing tumor.", "detaileddescription": "", - "website": "", + "website": "https://github.com/QTIM-Lab/DeepNeuro", "citation": "", "version": "0.1", "docker": { - "dockerhub_repository": "qtimlab/deepinfer_glioblastoma", + "dockerhub_repository": "qtimlab/deepneuro_segment_gbm", "digest": "", "size": "6.77 GB" }, - "model_name": "qtim_glioblastoma", + "model_name": "deepneuro_glioblastoma", "data_path": "/INPUT_DATA", "members": [ { @@ -55,17 +55,24 @@ "itk_type": "typename FilterType::SizeType" }, { - "name": "BiasCorrection", + "name": "debiased", "type": "bool", "default": "true", - "detaileddescriptionSet": "Apply N4BiasCorrection before segmentation.\n", + "detaileddescriptionSet": "If data is already debiased, check this box.\n", "iotype": "parameter" }, { - "name": "Preprocess", + "name": "resampled", "type": "bool", "default": "true", - "detaileddescriptionSet": "Co register and resample images to isotropic space before segmentation.\n", + "detaileddescriptionSet": "If data is already isotropically resampled, check this box.\n", + "iotype": "parameter" + }, + { + "name": "registered", + "type": "bool", + "default": "true", + "detaileddescriptionSet": "If data is already registered, check this box.\n", "iotype": "parameter" }, { @@ -78,4 +85,4 @@ "itk_type": "typename FilterType::SizeType" } ] -} \ No newline at end of file +} From 847604f84426a23ff8fe800fdf578bc63d371c09 Mon Sep 17 00:00:00 2001 From: Andrew Beers Date: Thu, 11 Jan 2018 16:13:16 -0500 Subject: [PATCH 3/4] Add SkullStripping option --- DeepNeuro_Glioblastoma.json | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/DeepNeuro_Glioblastoma.json b/DeepNeuro_Glioblastoma.json index 7dbfb9b..e344400 100644 --- a/DeepNeuro_Glioblastoma.json +++ b/DeepNeuro_Glioblastoma.json @@ -75,6 +75,13 @@ "detaileddescriptionSet": "If data is already registered, check this box.\n", "iotype": "parameter" }, + { + "name": "skullstripped", + "type": "bool", + "default": "true", + "detaileddescriptionSet": "If data is already skullstripped, check this box.\n", + "iotype": "parameter" + }, { "name": "Output", "type": "volume", From e04055323286a51ecffc0cac8f4d53d3be19326c Mon Sep 17 00:00:00 2001 From: AndrewBeers Date: Fri, 12 Jan 2018 10:46:32 -0500 Subject: [PATCH 4/4] Add gpu selector, rename parameters. --- DeepNeuro_Glioblastoma.json | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/DeepNeuro_Glioblastoma.json b/DeepNeuro_Glioblastoma.json index e344400..546a133 100644 --- a/DeepNeuro_Glioblastoma.json +++ b/DeepNeuro_Glioblastoma.json @@ -83,7 +83,23 @@ "iotype": "parameter" }, { - "name": "Output", + "name": "GPU Number", + "type": "uint16_t", + "iotype": "parameter", + "param_name": "gpu_num", + "default": 0 + }, + { + "name": "Output_WholeTumor", + "type": "volume", + "iotype": "output", + "voltype": "LabelMap", + "detaileddescriptionSet": "Output labelmap for the segmentation results.\n", + "default": "std::vector(3, 64)", + "itk_type": "typename FilterType::SizeType" + }, + { + "name": "Output_EnhancingTumor", "type": "volume", "iotype": "output", "voltype": "LabelMap", @@ -92,4 +108,4 @@ "itk_type": "typename FilterType::SizeType" } ] -} +} \ No newline at end of file