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Manual correction of MS lesion segmentation done by model #23

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plbenveniste opened this issue Jun 19, 2024 · 8 comments
Open

Manual correction of MS lesion segmentation done by model #23

plbenveniste opened this issue Jun 19, 2024 · 8 comments

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@plbenveniste
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In this issue, I detail the work done:

  • to get MS lesion segmentation using the current best model.
  • to manually correct those lesion segmentations

I created the file monai/run_inference.py to be able to run inference on a single image or on a list of images stored in a YML file the following way:

IMAGES:
- image/path/img.nii.gz
@plbenveniste
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plbenveniste commented Jun 19, 2024 •
edited
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I wanted to segment T2w sagital images from the dataset umass-ms-ge-pioneer3.

To get the list of images, I ran the following bash script:

#!/bin/bash

# Assign the output path from the argument
output_path="$1"

# Dataset path
dataset_path="$2"

# Define the output YAML file
output_file="$output_path/files_list.yml"

# Start the YAML file with the root element
echo "IMAGES:" > "$output_file"

# Find all files ending with "T2w" in the dataset path and append to the YAML file
find "$dataset_path" -type f -name "*T2w.nii.gz" | grep -v "ax" | while read -r file; do
    echo "  - $file" >> "$output_file"
done

echo "YAML file '$output_file' has been created with all files ending with 'T2w.nii.gz' and that don't contain 'ax'."

I ran it with the following command:

inference_results/get_inference_images.sh ~/ms_lesion_agnostic/inference_results/  ~/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/

Currently, running segmentation using the following command:

python ms-lesion-agnostic/monai/run_inference.py --config best_models/2024-04-24_15\:55\:43.704304/wandb/run-20240424_155544-2ll4wkgs/files/config.yaml  --data-path ~/ms_lesion_agnostic/inference_results/files_list.yml --output-dir inference_results/inference_umass_ms_ge_pioneer3_19_06_2024 --model-path best_models/2024-04-24_15\:55\:43.704304/best_model.pth/best_model.ckpt

@plbenveniste
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Here is the list of images which were segmented by the model:

Images to be segmented 
IMAGES:
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1083/ses-02/anat/sub-ms1083_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1083/ses-02/anat/sub-ms1083_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1083/ses-01/anat/sub-ms1083_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1083/ses-01/anat/sub-ms1083_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1313/ses-03/anat/sub-ms1313_ses-03_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1313/ses-03/anat/sub-ms1313_ses-03_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1313/ses-02/anat/sub-ms1313_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1313/ses-02/anat/sub-ms1313_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1313/ses-01/anat/sub-ms1313_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1313/ses-01/anat/sub-ms1313_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1141/ses-01/anat/sub-ms1141_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1141/ses-01/anat/sub-ms1141_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1207/ses-03/anat/sub-ms1207_ses-03_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1207/ses-03/anat/sub-ms1207_ses-03_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1207/ses-02/anat/sub-ms1207_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1207/ses-02/anat/sub-ms1207_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1207/ses-01/anat/sub-ms1207_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1207/ses-01/anat/sub-ms1207_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1044/ses-02/anat/sub-ms1044_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1044/ses-02/anat/sub-ms1044_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1044/ses-01/anat/sub-ms1044_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1044/ses-01/anat/sub-ms1044_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1287/ses-02/anat/sub-ms1287_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1287/ses-02/anat/sub-ms1287_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1287/ses-01/anat/sub-ms1287_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1287/ses-01/anat/sub-ms1287_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1210/ses-01/anat/sub-ms1210_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1210/ses-01/anat/sub-ms1210_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1242/ses-02/anat/sub-ms1242_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1242/ses-02/anat/sub-ms1242_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1242/ses-01/anat/sub-ms1242_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1242/ses-01/anat/sub-ms1242_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1274/ses-01/anat/sub-ms1274_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1274/ses-01/anat/sub-ms1274_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1119/ses-03/anat/sub-ms1119_ses-03_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1119/ses-03/anat/sub-ms1119_ses-03_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1119/ses-02/anat/sub-ms1119_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1119/ses-02/anat/sub-ms1119_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1119/ses-04/anat/sub-ms1119_ses-04_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1119/ses-04/anat/sub-ms1119_ses-04_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1119/ses-01/anat/sub-ms1119_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1119/ses-01/anat/sub-ms1119_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1156/ses-02/anat/sub-ms1156_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1156/ses-02/anat/sub-ms1156_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1156/ses-01/anat/sub-ms1156_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1156/ses-01/anat/sub-ms1156_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1005/ses-01/anat/sub-ms1005_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1005/ses-01/anat/sub-ms1005_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1065/ses-03/anat/sub-ms1065_ses-03_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1065/ses-03/anat/sub-ms1065_ses-03_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1065/ses-02/anat/sub-ms1065_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1065/ses-02/anat/sub-ms1065_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1065/ses-04/anat/sub-ms1065_ses-04_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1065/ses-04/anat/sub-ms1065_ses-04_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1065/ses-01/anat/sub-ms1065_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1065/ses-01/anat/sub-ms1065_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1062/ses-02/anat/sub-ms1062_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1062/ses-02/anat/sub-ms1062_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1062/ses-01/anat/sub-ms1062_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1062/ses-01/anat/sub-ms1062_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1298/ses-02/anat/sub-ms1298_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1298/ses-02/anat/sub-ms1298_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1298/ses-01/anat/sub-ms1298_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1298/ses-01/anat/sub-ms1298_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1070/ses-03/anat/sub-ms1070_ses-03_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1070/ses-03/anat/sub-ms1070_ses-03_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1070/ses-02/anat/sub-ms1070_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1070/ses-02/anat/sub-ms1070_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1070/ses-01/anat/sub-ms1070_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1070/ses-01/anat/sub-ms1070_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1128/ses-01/anat/sub-ms1128_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1128/ses-01/anat/sub-ms1128_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1176/ses-01/anat/sub-ms1176_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1176/ses-01/anat/sub-ms1176_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1016/ses-01/anat/sub-ms1016_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1016/ses-01/anat/sub-ms1016_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1322/ses-01/anat/sub-ms1322_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1322/ses-01/anat/sub-ms1322_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1328/ses-01/anat/sub-ms1328_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1328/ses-01/anat/sub-ms1328_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1248/ses-02/anat/sub-ms1248_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1248/ses-02/anat/sub-ms1248_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1248/ses-01/anat/sub-ms1248_ses-01_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1248/ses-01/anat/sub-ms1248_ses-01_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1182/ses-05/anat/sub-ms1182_ses-05_acq-STIR_T2w.nii.gz
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  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1182/ses-03/anat/sub-ms1182_ses-03_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1182/ses-02/anat/sub-ms1182_ses-02_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1182/ses-02/anat/sub-ms1182_ses-02_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1182/ses-04/anat/sub-ms1182_ses-04_acq-STIR_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1182/ses-04/anat/sub-ms1182_ses-04_T2w.nii.gz
  - /home/GRAMES.POLYMTL.CA/p119007/ms_lesion_agnostic/data/umass-ms-ge-pioneer3/sub-ms1299/ses-02/anat/sub-ms1299_ses-02_acq-STIR_T2w.nii.gz
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@plbenveniste
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Here are two example of "successful" predictions by the model:
ezgif com-animated-gif-maker (15)
ezgif com-animated-gif-maker (16)

@plbenveniste
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The segmentations are stored in duke/temp/plben/ms-lesion-agnostic/ms_seg_manual_correction/inference_umass_ms_ge_pioneer3_19_06_2024

@maxradx Could you manually correcting some of them so that I can then add them in the training of my model ?
Also, if you could give some feedback on the model outputs in general, that would be great !
Thanks 😄

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maxradx commented Jun 29, 2024

Hi @plbenveniste
Thanks for asking.
Video of qualitative assessment of the performance of the model linked here.
Will be able to manual correct in my next research block (especially if the 3D Slicer module will be able to do efficient manual correction)
Cheers,
Maxime

@plbenveniste
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Thanks a lot @maxradx for your screen recording! Your feedback is very useful 😃

Here is some note from Maxime's video:

  • the model doesn't correctly segment the boundaries of the lesion (this is an expected behavior because of inter/intra rater variability)
  • the model tends to merge lesions instead of having multiple lesions close by. (expected behavior: question of 1 big lesion or confluent lesion?)
  • on T2w images the model struggles more than on STIR images (expected because easier to see lesions on T2w than on PSIR with the human eye)
  • model partially worked even on corrupted image (That's great news)
  • on STIR: accurately identifies the correct number of lesions but doesn't identify precisely the lesion boundaries
  • on T2w: it's harder for human (and it seems for the model as well) to identify lesions on T2w than on PSIR but the model still performs relatively well

@jcohenadad This video could be a good demo of the current state of our model. If it's alright with @maxradx we coud maybe share it with some collaborators to show the progress we have made, and maybe they would have some feedback as well. What do you think?

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This video could be a good demo of the current state of our model. If it's alright with @maxradx we coud maybe share it with some collaborators to show the progress we have made, and maybe they would have some feedback as well. What do you think?

Very nice video indeed. However I would not share because:

  • it is in French
  • asking them to watch a 23min video is not worth their time-- I would rather send them a progress report, or better, a manuscript draft (see 3rd point)
  • collaborators are mostly interested in getting this published and be coauthored, so what would be more interesting/useful from their perspective is to get some model performance summary being drafted for a conference/journal paper

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maxradx commented Jul 7, 2024

I agree with above.
I think also it should not be shared (for now) --- progress report will be better.
When I will come back, I can dedicate time to re-assess in a more formal way (this video was really a 'real-time' unprepared assessment) -- Also, it would be great to have features in the 3D Slicer module (see repo) so I could directly manually correct time in a time-efficient way!
Cheers,

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@jcohenadad @plbenveniste @maxradx