Anirudh Balaraman commited on
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d60f76e
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1 Parent(s): bae28ee

Fix typos and enhance clarity in pipeline.md

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Correct typos and improve clarity in the pipeline documentation.

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  1. docs/pipeline.md +7 -8
docs/pipeline.md CHANGED
@@ -11,11 +11,11 @@ flowchart TD
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  end
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  subgraph Stage 1
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- P[PI-RADS Training\nCrossEntropy + Attention Loss]
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  end
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  subgraph Stage 2
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- C[csPCa Training\nFrozen Backbone + BCE Loss]
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  end
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  G --> P
@@ -23,18 +23,17 @@ flowchart TD
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  ```
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  ## Preprocessing
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-
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- Run all four steps in sequence:
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-
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  ```bash
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  python preprocess_main.py \
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  --config config/config_preprocess.yaml \
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  --steps register_and_crop get_segmentation_mask histogram_match get_heatmap
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  ```
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  ### Step 1: Register and Crop
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- Resamples T2, DWI, and ADC to a common spacing of `(0.4, 0.4, 3.0)` mm using `picai_prep`, then center-crops with a configurable margin (default 20%).
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  ### Step 2: Prostate Segmentation
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@@ -42,11 +41,11 @@ Runs a pre-trained segmentation model on T2W images to generate binary prostate
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  ### Step 3: Histogram Matching
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- Matches the intensity histogram of each modality to a reference image within masked (prostate) regions using `skimage.exposure.match_histograms`.
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  ### Step 4: Heatmap Generation
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- Creates attention heatmaps from DWI and ADC:
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  - **DWI heatmap**: `(dwi - min) / (max - min)` — higher DWI signal = higher attention
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  - **ADC heatmap**: `(max - adc) / (max - min)` — lower ADC = higher attention (inverted)
 
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  end
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  subgraph Stage 1
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+ P[PI-RADS Training \n CrossEntropy + Attention Loss]
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  end
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  subgraph Stage 2
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+ C[csPCa Training \n Frozen Backbone + BCE Loss]
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  end
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  G --> P
 
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  ```
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  ## Preprocessing
 
 
 
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  ```bash
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  python preprocess_main.py \
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  --config config/config_preprocess.yaml \
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  --steps register_and_crop get_segmentation_mask histogram_match get_heatmap
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  ```
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+ Run the following steps in sequnce:
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+
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  ### Step 1: Register and Crop
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+ Resamples T2W, DWI, and ADC to a common spacing of `(0.4, 0.4, 3.0)` mm using `picai_prep`, then center-crops with a configurable margin (default 20%).
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  ### Step 2: Prostate Segmentation
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  ### Step 3: Histogram Matching
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+ Matches the histogram intensity of each sequnce to a reference image within masked (prostate) regions using `skimage.exposure.match_histograms`.
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  ### Step 4: Heatmap Generation
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+ Creates weak-attention heatmaps from DWI and ADC:
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  - **DWI heatmap**: `(dwi - min) / (max - min)` — higher DWI signal = higher attention
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  - **ADC heatmap**: `(max - adc) / (max - min)` — lower ADC = higher attention (inverted)