BAMF Lung and FDG-Avid Tumor #86

jithenece · 2024-07-01T20:57:00Z

Pretrained model for 3D semantic image segmentation of the FDG-avid lesions from PT/CT scans

jithenece · 2024-07-02T05:53:07Z

sample:
  idc_version: Version 5: Updated 2020/12/22
  data:
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.6655.2359.184691786899278131062806456462
    aws_url: s3://idc-open-data/aafd2a22-6236-4eff-b541-1dfd8de923e8/*
    path: case_study1/ct
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.6655.2359.168809572664004911257595338967
    aws_url: s3://idc-open-data/c6ff3b5f-eb4d-4a08-8e6b-3004b2ebbc0f/*
    path: case_study1/pt

reference:
  url: https://drive.google.com/file/d/1jcujIoSvYG0Owps8nZVBBbjSGnCk7Wdx/view?usp=sharing

jithenece · 2024-07-02T06:01:17Z

screenshots.zip

Added screenshots

jithenece · 2024-07-02T06:02:30Z

@LennyN95 could someone review this so that i can do similar fixes for other PRs and submit?

LennyN95

Overall great implementation. I've made some points on the usage of TS as part of this model that I'd like to discuss briefly before moving forward.

models/bamf_pet_ct_lung_tumor/config/default.yml

models/bamf_pet_ct_lung_tumor/utils/LungPostProcessor.py

models/bamf_pet_ct_lung_tumor/config/default.yml

models/bamf_pet_ct_lung_tumor/utils/NNUnetPETCTRunner.py

LennyN95

Looks good! Some minor suggestions below.

models/bamf_pet_ct_lung_tumor/utils/LungSegmentatorRunner.py

models/bamf_pet_ct_lung_tumor/config/default.yml

models/bamf_pet_ct_lung_tumor/utils/LungSegmentatorRunner.py

jithenece · 2024-08-08T08:00:10Z

/review

@LennyN95 Please review and let me know for more changes.

jithenece · 2024-08-08T08:06:05Z

/test

sample:
  idc_version: Version 5: Updated 2020/12/22
  data:
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.6655.2359.184691786899278131062806456462
    aws_url: s3://idc-open-data/aafd2a22-6236-4eff-b541-1dfd8de923e8/*
    path: 'case_study1/ct'
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.6655.2359.168809572664004911257595338967
    aws_url: s3://idc-open-data/c6ff3b5f-eb4d-4a08-8e6b-3004b2ebbc0f/*
    path: 'case_study1/pt'

reference:
  url: https://drive.google.com/file/d/1MGe1dR22GF-oF7BwQ4bE3Oq-9KBnohku

jithenece · 2024-08-08T08:12:21Z

/test

sample:
  idc_version: "Data Release 5.0 December 22, 2020"
  data:
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.6655.2359.184691786899278131062806456462
    aws_url: s3://idc-open-data/aafd2a22-6236-4eff-b541-1dfd8de923e8/*
    path: 'case_study1/ct'
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.6655.2359.168809572664004911257595338967
    aws_url: s3://idc-open-data/c6ff3b5f-eb4d-4a08-8e6b-3004b2ebbc0f/*
    path: 'case_study1/pt'

reference:
  url: https://drive.google.com/file/d/1MGe1dR22GF-oF7BwQ4bE3Oq-9KBnohku/view?usp=sharing

jithenece · 2024-08-29T10:14:48Z

/test

attaching segmentation
output.zip

sample:
  idc_version: 15.0
  data:
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.4334.1501.322501480363502116767369539775
    aws_url: s3://idc-open-data/7d19e1ee-f2c9-4158-a6e2-d093468e393b/*
    path: case1/ct
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.4334.1501.329094085186214039017114090511
    aws_url: s3://idc-open-data/c39ec1fc-f5d3-4685-9077-dafd79bc5970/*
    path: case1/pt

reference:
  url: https://github.com/user-attachments/files/16797384/output.zip

Test Results (24.08.29_15.15.30_AkoraywFNq)

id: 02819301-0b3b-4324-9723-77207b8708d6
date: '2024-08-29 16:21:07'
checked_files:
- file: bamf_pet_ct_lung_tumor.seg.dcm
  path: /app/test/src/case1/bamf_pet_ct_lung_tumor.seg.dcm
  checks:
  - checker: DicomsegContentCheck
    notes:
    - label: Segment Count
      description: The number of segments identified in the inspected dicomseg file.
      info: 2
    findings:
    - label: Dice Score Difference
      description: Dice score between reference and test image
      subpath: 'segment #1'
      info: 0.975907953098239
summary:
  files_missing: 0
  files_extra: 0
  checks:
    DicomsegContentCheck:
      files: 1
      findings:
        Dice Score Difference: 1
conclusion: false

jithenece · 2024-09-09T08:23:32Z

/test

attaching segmentation
output.zip

sample:
  idc_version: 15.0
  data:
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.4334.1501.322501480363502116767369539775
    aws_url: s3://idc-open-data/7d19e1ee-f2c9-4158-a6e2-d093468e393b/*
    path: case1/ct
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.4334.1501.329094085186214039017114090511
    aws_url: s3://idc-open-data/c39ec1fc-f5d3-4685-9077-dafd79bc5970/*
    path: case1/pt

reference:
  url: https://github.com/user-attachments/files/16927593/output.zip

LennyN95 · 2024-09-19T13:41:22Z

@jithenece the test results suggest there is a quite high difference (DiceScore), could you elaborate on this?

Please note, we updated our base image. All mhub dependencies are now installed in a virtual environment under /app/.venv running Python 3.11. Python, virtual environment and dependencies are now managed with uv. If required, you can create custom virtual environments, e.g., uv venv -p 3.8 .venv38 and use uv pip install -p .venv38 packge-name to install dependencies and uv run -p .venv3.8 python script.py to run a python script.

We also simplified our test routine. Sample and reference data now have to be uploaded to Zenodo and provided in a mhub.tom file at the project root. The process how to create and provide these sample data is explained in the updated testing phase article of our documentation. Under doi.org/10.5281/zenodo.13785615 we provide sample data as a reference.

LennyN95 · 2025-02-17T13:20:28Z

Test Results

id: 37a30205-aa3f-489a-87f2-1228eb9c6947
name: MHub Test Report (default)
date: '2025-02-17 14:20:24'
missing_files:
- case1/bamf_pet_ct_lung_tumor.seg.dcm
summary:
  files_missing: 1
  files_extra: 0
  checks: {}
conclusion: false

LennyN95 · 2025-02-17T16:48:56Z

@jithenece NNUnet installs torch 2.2.6 now, which introduces a breaking change. Please replace your RUN pip3 install ... with this: RUN uv pip install p_tqdm==1.4 TotalSegmentator==1.5.7 nnunet==1.6.6 torch==2.2.2 --no-cache-dir, testing then should work. If possible, you can also allow repository maintainers access to your fork. Once this is updated, I will re-run the test. Thanks!

vanossj · 2025-02-18T13:17:34Z

@LennyN95 invite sent

- pin torch to v2.2.2

LennyN95 · 2025-02-18T15:53:58Z

Test Results

id: bada4f00-19d9-437d-9532-74e540bbbf1a
name: MHub Test Report (default)
date: '2025-02-18 16:53:55'
checked_files:
- file: bamf_pet_ct_lung_tumor.seg.dcm
  path: /app/data/output_data/case1/bamf_pet_ct_lung_tumor.seg.dcm
  checks:
  - checker: DicomsegContentCheck
    notes:
    - label: Segment Count
      description: The number of segments identified in the inspected dicomseg file.
      info: 2
summary:
  files_missing: 0
  files_extra: 0
  checks:
    DicomsegContentCheck:
      files: 1
conclusion: true

jithenece added 14 commits May 1, 2024 13:46

create PET CT multi modality nnUnetRunner

25c975f

Resampler module

74232c5

define flow

5167ae4

use FDG_AVID_TUMOR entry

ec8ba04

add meta information

aa3d6d7

update label info

8dcbd53

fix entrypoint

ef8433a

Merge branch 'MHubAI:main' into bamf_nnunet_pet_ct_lung

b0024ed

update results stats

3660f06

change post-processing logic

d118d3f

comments

3e84dd9

format logic

ea50a98

rename the folder

5a3ba63

comments updated

0f7bb8c

jithenece marked this pull request as ready for review July 2, 2024 06:01

use NiftiConverter

f9e1456

LennyN95 self-requested a review July 12, 2024 13:35

LennyN95 requested changes Jul 24, 2024

View reviewed changes

fix review comments

670823d

LennyN95 requested changes Jul 30, 2024

View reviewed changes

models/bamf_pet_ct_lung_tumor/utils/LungSegmentatorRunner.py Show resolved Hide resolved

models/bamf_pet_ct_lung_tumor/config/default.yml Outdated Show resolved Hide resolved

models/bamf_pet_ct_lung_tumor/utils/LungSegmentatorRunner.py Outdated Show resolved Hide resolved

jithenece added 3 commits July 30, 2024 23:57

update dcm2niix to fix conversion errors

1f12571

extract lung only segments from ts

c9b74f8

fix pip errors

effdccc

github-actions bot added the REQUEST REVIEW Attach this label to your PR when your submission is "in progress" and is ready to be reviewed by us label Aug 8, 2024

github-actions bot added the INVALID TEST REQUEST The contributor requested a test but the test block is not valid. label Aug 8, 2024

github-actions bot added TEST REQUESTED and removed INVALID TEST REQUEST The contributor requested a test but the test block is not valid. labels Aug 8, 2024

jithenece mentioned this pull request Aug 21, 2024

BAMF Liver and Tumor segmentation #84

Open

jithenece added 2 commits August 23, 2024 18:51

remove dcm2niix

d781beb

Merge branch 'MHubAI:main' into bamf_pet_ct_lung_tumor

a65489e

github-actions bot added INVALID TEST REQUEST The contributor requested a test but the test block is not valid. TEST REQUESTED and removed TEST REQUESTED INVALID TEST REQUEST The contributor requested a test but the test block is not valid. labels Sep 9, 2024

Merge branch 'MHubAI:main' into bamf_pet_ct_lung_tumor

368654a

jithenece added 2 commits October 2, 2024 04:21

Merge branch 'MHubAI:main' into bamf_pet_ct_lung_tumor

0f43346

/test validation

3a4ee41

LennyN95 removed the TEST REQUESTED label Feb 17, 2025

Update Dockerfile

7223fee

- pin torch to v2.2.2

LennyN95 approved these changes Feb 18, 2025

View reviewed changes

LennyN95 merged commit 197ae68 into MHubAI:main Feb 18, 2025
1 check passed

BAMF Lung and FDG-Avid Tumor #86

BAMF Lung and FDG-Avid Tumor #86

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