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Merge pull request #14 from niivue/lint
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Lint
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@neurolabusc
neurolabusc authored May 15, 2024
2 parents 70b86bf + cc0f1e4 commit bd1be6f
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Showing 33 changed files with 685 additions and 2,180 deletions.
839 changes: 36 additions & 803 deletions brainchop-mainthread.js
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34 changes: 2 additions & 32 deletions brainchop-parameters.js
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Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,6 @@ const inferenceModelsList = [
type: 'Segmentation',
path: '/models/model5_gw_ae/model.json',
modelName: '\u26A1 Tissue GWM (light)',
labelsPath: './models/model5_gw_ae/labels.json',
colorsPath: './models/model5_gw_ae/colorLUT.json',
colormapPath: './models/model5_gw_ae/colormap3.json',
preModelId: null, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -52,8 +50,6 @@ const inferenceModelsList = [
type: 'Segmentation',
path: '/models/model20chan3cls/model.json',
modelName: '\u{1F52A} Tissue GWM (High Acc)',
labelsPath: './models/model20chan3cls/labels.json',
colorsPath: './models/model20chan3cls/colorLUT.json',
colormapPath: './models/model20chan3cls/colormap.json',
preModelId: null, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -78,8 +74,6 @@ const inferenceModelsList = [
type: 'Segmentation',
path: '/models/model20chan3cls/model.json',
modelName: '\u{1F52A} Tissue GWM (High Acc, Low Mem)',
labelsPath: './models/model20chan3cls/labels.json',
colorsPath: './models/model20chan3cls/colorLUT.json',
colormapPath: './models/model20chan3cls/colormap.json',
preModelId: null, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -104,8 +98,6 @@ const inferenceModelsList = [
type: 'Atlas',
path: '/models/model30chan18cls/model.json',
modelName: '\u{1FA93} Subcortical + GWM (High Mem, Fast)',
labelsPath: './models/model30chan18cls/labels.json',
colorsPath: './models/model30chan18cls/colorLUT.json',
colormapPath: './models/model30chan18cls/colormap.json',
preModelId: null, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -130,8 +122,6 @@ const inferenceModelsList = [
type: 'Atlas',
path: '/models/model30chan18cls/model.json',
modelName: '\u{1FA93} Subcortical + GWM (Low Mem, Slow)',
labelsPath: './models/model30chan18cls/labels.json',
colorsPath: './models/model30chan18cls/colorLUT.json',
colormapPath: './models/model30chan18cls/colormap.json',
preModelId: null, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -156,8 +146,6 @@ const inferenceModelsList = [
type: 'Atlas',
path: '/models/model18cls/model.json',
modelName: '\u{1FA93} Subcortical + GWM (Low Mem, Faster)',
labelsPath: './models/model18cls/labels.json',
colorsPath: './models/model18cls/colorLUT.json',
colormapPath: './models/model18cls/colormap.json',
preModelId: null, // model run first e.g. Brain_Extraction { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -182,8 +170,6 @@ const inferenceModelsList = [
type: 'Atlas',
path: '/models/model30chan18cls/model.json',
modelName: '\u{1F52A}\u{1FA93} Subcortical + GWM (Failsafe, Less Acc)',
labelsPath: './models/model30chan18cls/labels.json',
colorsPath: './models/model30chan18cls/colorLUT.json',
colormapPath: './models/model30chan18cls/colormap.json',
preModelId: 1, // model run first e.g. Brain_Extraction { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -208,8 +194,6 @@ const inferenceModelsList = [
type: 'Atlas',
path: '/models/model30chan50cls/model.json',
modelName: '\u{1F52A} Aparc+Aseg 50 (High Mem, Fast)',
labelsPath: './models/model30chan50cls/labels.json',
colorsPath: './models/model30chan50cls/colorLUT.json',
colormapPath: './models/model30chan50cls/colormap.json',
preModelId: 1, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -234,8 +218,6 @@ const inferenceModelsList = [
type: 'Atlas',
path: '/models/model30chan50cls/model.json',
modelName: '\u{1F52A} Aparc+Aseg 50 (Low Mem, Slow)',
labelsPath: './models/model30chan50cls/labels.json',
colorsPath: './models/model30chan50cls/colorLUT.json',
colormapPath: './models/model30chan50cls/colormap.json',
preModelId: 1, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -261,8 +243,6 @@ const inferenceModelsList = [
type: 'Brain_Extraction',
path: '/models/model5_gw_ae/model.json',
modelName: '\u26A1 Extract the Brain (FAST)',
labelsPath: null,
colorsPath: null,
preModelId: null, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
isBatchOverlapEnable: false, // create extra overlap batches for inference
Expand All @@ -285,8 +265,6 @@ const inferenceModelsList = [
type: 'Brain_Extraction',
path: '/models/model11_gw_ae/model.json',
modelName: '\u{1F52A} Extract the Brain (High Acc, Slow)',
labelsPath: null,
colorsPath: null,
preModelId: null, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
isBatchOverlapEnable: false, // create extra overlap batches for inference
Expand All @@ -310,8 +288,6 @@ const inferenceModelsList = [
type: 'Brain_Masking',
path: '/models/model5_gw_ae/model.json',
modelName: '\u26A1 Brain Mask (FAST)',
labelsPath: null,
colorsPath: null,
colormapPath: './models/model5_gw_ae/colormap.json',
preModelId: null, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
Expand All @@ -335,8 +311,6 @@ const inferenceModelsList = [
type: 'Brain_Masking',
path: '/models/model11_gw_ae/model.json',
modelName: '\u{1F52A} Brain Mask (High Acc, Low Mem)',
labelsPath: null,
colorsPath: null,
preModelId: null, // Model run first e.g. crop the brain { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
isBatchOverlapEnable: false, // create extra overlap batches for inference
Expand All @@ -360,10 +334,8 @@ const inferenceModelsList = [
type: 'Atlas',
path: '/models/model21_104class/model.json',
modelName: '\u{1F52A} Aparc+Aseg 104 (High Mem, Fast)',
labelsPath: './models/model21_104class/labels.json',
colorsPath: './models/model21_104class/colorLUT.json',
colormapPath: './models/model21_104class/colormap.json',
preModelId: 1, // model run first e.g. Brain_Extraction { null, 1, 2, .. }
preModelId: 0, // model run first e.g. Brain_Extraction { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
isBatchOverlapEnable: false, // create extra overlap batches for inference
numOverlapBatches: 200, // Number of extra overlap batches for inference
Expand All @@ -386,10 +358,8 @@ const inferenceModelsList = [
type: 'Atlas',
path: '/models/model21_104class/model.json',
modelName: '\u{1F52A} Aparc+Aseg 104 (Low Mem, Slow)',
labelsPath: './models/model21_104class/labels.json',
colorsPath: './models/model21_104class/colorLUT.json',
colormapPath: './models/model21_104class/colormap.json',
preModelId: 1, // model run first e.g. Brain_Extraction { null, 1, 2, .. }
preModelId: 0, // model run first e.g. Brain_Extraction { null, 1, 2, .. }
preModelPostProcess: false, // If true, perform postprocessing to remove noisy regions after preModel inference generate output.
isBatchOverlapEnable: false, // create extra overlap batches for inference
numOverlapBatches: 200, // Number of extra overlap batches for inference
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