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Merged
davidmeunier79 merged 13 commits into from
Apr 30, 2025
Merged

Add itk debias #299

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6b86770
added rigid_flag
davidmeunier79 Dec 10, 2024
bb861d6
itk_debias
davidmeunier79 Dec 11, 2024
ea60bd1
debias over padded image
davidmeunier79 Dec 11, 2024
5a69e70
output mask
davidmeunier79 Dec 11, 2024
0a976ba
Merge branch 'master' into add_itk_debias
davidmeunier79 Dec 16, 2024
87a1578
rename gcc node
davidmeunier79 Dec 17, 2024
9a80acd
seg_pipe.connect(data_preparation_pipe, "outputnode.stereo_padded_T1",
davidmeunier79 Dec 18, 2024
bbcf91b
10-rc1
davidmeunier79 Apr 29, 2025
2f1c98b
Merge branch 'master' into add_itk_debias
davidmeunier79 Apr 29, 2025
cddf982
clean Dockerfiles
davidmeunier79 Apr 30, 2025
63a47f8
ANTS_robust_reg
davidmeunier79 Apr 30, 2025
35749b2
baboon0
davidmeunier79 Apr 30, 2025
9e2a81f
reorg
davidmeunier79 Apr 30, 2025
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68 changes: 56 additions & 12 deletions .github/workflows/build_on_prerelease.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ jobs:
uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
with:
context: .
file: Dockerfile_testpypi_nomcr
file: Dockerfile_testpypi
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
Expand Down Expand Up @@ -161,7 +161,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results

run-pretest-ants-marmo:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg marmo)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand All @@ -187,9 +187,9 @@ jobs:
ls macapype_CI_v2.1/cerimed_marmo
echo ""

- name: Running test pipeline cerimed_marmo ANTS_robustreg_noseg T1 T2
- name: Running test pipeline cerimed_marmo ANTS_noseg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_robustreg_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/

Expand All @@ -206,7 +206,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results

run-pretest-ants-marmoT2:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS marmo T2)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo T2)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -250,7 +250,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results

run-pretest-ants-baboon:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -294,7 +294,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results

run-pretest-ants-baboon3:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -338,7 +338,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3

run-pretest-ants-baboon2:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -382,7 +382,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2

run-pretest-ants-baboon1:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -425,6 +425,50 @@ jobs:
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1

run-pretest-ants-baboon0:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440

steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest

- name: Download dataset
run: |

curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip

unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1

pwd
echo ""

ls macapype_CI_v2.1
echo ""

ls macapype_CI_v2.1/cerimed_baboon
echo ""

- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results0 -soft ANTS_robustreg_prep -species baboon0 -sub Prune -ses 0 -deriv -pad -dt T1 T2

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/sub-Prune/ses-0/anat/
echo ""

- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0

run-pretest-ants-baboon3-0p6:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
needs: docker-build
Expand Down Expand Up @@ -452,7 +496,7 @@ jobs:
ls macapype_CI_v2.1/cerimed_baboon
echo ""

- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results3 -soft ANTS_robustreg -species baboon3_0p6 -sub Prune -ses 3 -deriv -pad -dt T1 T2

Expand Down Expand Up @@ -496,7 +540,7 @@ jobs:
ls macapype_CI_v2.1/cerimed_baboon
echo ""

- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results2 -soft ANTS_robustreg -species baboon2_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2

Expand Down Expand Up @@ -540,7 +584,7 @@ jobs:
ls macapype_CI_v2.1/cerimed_baboon
echo ""

- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results1 -soft ANTS_robustreg -species baboon1_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2

Expand Down
68 changes: 56 additions & 12 deletions .github/workflows/build_on_release.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ jobs:
with:
context: .

file: Dockerfile_nomcr
file: Dockerfile
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
Expand Down Expand Up @@ -161,7 +161,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results

run-pretest-ants-marmo:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg marmo)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand All @@ -187,9 +187,9 @@ jobs:
ls macapype_CI_v2.1/cerimed_marmo
echo ""

- name: Running test pipeline cerimed_marmo ANTS_robustreg_noseg T1 T2
- name: Running test pipeline cerimed_marmo ANTS_noseg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_robustreg_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/

Expand All @@ -206,7 +206,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results

run-pretest-ants-marmoT2:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS marmo T2)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo T2)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -250,7 +250,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results

run-pretest-ants-baboon:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -294,7 +294,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results

run-pretest-ants-baboon3:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -338,7 +338,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3

run-pretest-ants-baboon2:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -382,7 +382,7 @@ jobs:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2

run-pretest-ants-baboon1:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440
Expand Down Expand Up @@ -425,6 +425,50 @@ jobs:
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1

run-pretest-ants-baboon0:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
needs: docker-build
runs-on: ubuntu-latest
timeout-minutes: 1440

steps:
- name: Pull latest docker image
run:
docker pull macatools/macapype:latest

- name: Download dataset
run: |

curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip

unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1

pwd
echo ""

ls macapype_CI_v2.1
echo ""

ls macapype_CI_v2.1/cerimed_baboon
echo ""

- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results0 -soft ANTS_robustreg_prep -species baboon0 -sub Prune -ses 0 -deriv -pad -dt T1 T2

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/

ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/sub-Prune/ses-0/anat/
echo ""

- name: Cleaning dataset
run:
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0

run-pretest-ants-baboon3-0p6:
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
needs: docker-build
Expand Down Expand Up @@ -452,7 +496,7 @@ jobs:
ls macapype_CI_v2.1/cerimed_baboon
echo ""

- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results3 -soft ANTS_robustreg -species baboon3_0p6 -sub Prune -ses 3 -deriv -pad -dt T1 T2

Expand Down Expand Up @@ -496,7 +540,7 @@ jobs:
ls macapype_CI_v2.1/cerimed_baboon
echo ""

- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results2 -soft ANTS_robustreg -species baboon2_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2

Expand Down Expand Up @@ -540,7 +584,7 @@ jobs:
ls macapype_CI_v2.1/cerimed_baboon
echo ""

- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
run: |
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results1 -soft ANTS_robustreg -species baboon1_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2

Expand Down
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