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Diagnose ds210 failure #2731

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merged 5 commits into from
Apr 21, 2022
Merged

Diagnose ds210 failure #2731

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eb0b80e
CI: Set random seed to match a failing build
effigies Mar 3, 2022
fae2c19
DBG: Test masking workflow updates
mgxd Apr 19, 2022
04dbcb5
CI: Increase circle machine limits
mgxd Apr 20, 2022
2da7d2e
MAINT: Bump in-house dependencies
mgxd Apr 21, 2022
916022f
FIX: Remove fixed seed [skip tests] [skip ds005] [skip ds054]
mgxd Apr 21, 2022
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30 changes: 17 additions & 13 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ jobs:
# upgrade Docker version
image: ubuntu-2004:202104-01
working_directory: /tmp/src/fmriprep
resource_class: large
steps:
- checkout
- run:
Expand Down Expand Up @@ -354,6 +355,7 @@ jobs:
machine:
image: ubuntu-2004:202104-01
working_directory: /tmp/ds005
resource_class: large
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
- DATASET: ds005
Expand Down Expand Up @@ -448,8 +450,8 @@ jobs:
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
--skull-strip-template OASIS30ANTs:res-1 \
--output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \
--sloppy --write-graph --mem_mb 4096 \
--nthreads 2 --anat-only -vv
--sloppy --write-graph --mem-mb 14336 \
--nthreads 4 --anat-only -vv
fi
- run:
name: Clean-up after anatomical run
Expand Down Expand Up @@ -490,11 +492,11 @@ jobs:
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
${FASTRACK_ARG} \
--output-layout legacy \
--sloppy --write-graph --mem_mb 4096 \
--sloppy --write-graph --mem-mb 14336 \
--skull-strip-template OASIS30ANTs:res-1 \
--output-spaces fsaverage5 fsnative \
--use-plugin /home/circleci/src/fmriprep/.circleci/legacy.yml \
--nthreads 2 -vv
--nthreads 4 -vv
- store_artifacts:
path: /tmp/ds005/derivatives
- run:
Expand Down Expand Up @@ -534,9 +536,9 @@ jobs:
--config $PWD/nipype.cfg -w /tmp/${DATASET}/work_bids \
/tmp/data/${DATASET}/ /tmp/${DATASET}/bids participant \
${FASTRACK_ARG} \
--sloppy --write-graph --mem_mb 4096 \
--sloppy --write-graph --mem-mb 14336 \
--output-spaces fsaverage5 \
--nthreads 2 -vv
--nthreads 4 -vv
- run:
name: Checking outputs of partial fMRIPrep run
command: |
Expand Down Expand Up @@ -565,10 +567,10 @@ jobs:
--fs-subjects-dir /tmp/${DATASET}/freesurfer \
${FASTRACK_ARG} \
--output-layout legacy \
--sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
--sloppy --write-graph --use-syn-sdc --mem-mb 14336 \
--output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
--aroma-melodic-dimensionality 2 --use-aroma \
--nthreads 2 --cifti-output -vv
--nthreads 4 --cifti-output -vv
- run:
name: Checking outputs of partial fMRIPrep run
command: |
Expand Down Expand Up @@ -605,6 +607,7 @@ jobs:
machine:
image: ubuntu-2004:202104-01
working_directory: /tmp/ds054
resource_class: large
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
- DATASET: ds054
Expand Down Expand Up @@ -692,7 +695,7 @@ jobs:
--output-layout legacy \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem_mb 4096 --nthreads 2 --anat-only -vv
--mem-mb 14336 --nthreads 4 --anat-only -vv
fi
- run:
name: Clean-up after anatomical run
Expand Down Expand Up @@ -721,7 +724,7 @@ jobs:
--output-layout legacy \
--fs-no-reconall --sloppy \
--output-spaces MNI152NLin2009cAsym:res-2 anat func \
--mem_mb 4096 --nthreads 2 -vv --debug compcor
--mem-mb 14336 --nthreads 4 -vv --debug compcor
- run:
name: Checking outputs of fMRIPrep
command: |
Expand Down Expand Up @@ -774,6 +777,7 @@ jobs:
machine:
image: ubuntu-2004:202104-01
working_directory: /tmp/ds210
resource_class: large
environment:
- FS_LICENSE: /tmp/fslicense/license.txt
- DATASET: ds210
Expand All @@ -787,7 +791,7 @@ jobs:
set -x +e
COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)"
DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')"
SKIP_DS210="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds054\]' )"
SKIP_DS210="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds210\]' )"
if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then
echo "Only docs build"
circleci step halt
Expand Down Expand Up @@ -861,7 +865,7 @@ jobs:
--output-layout legacy \
--fs-no-reconall --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem_mb 4096 --nthreads 2 --anat-only -vv
--mem-mb 14336 --nthreads 4 --anat-only -vv
fi
- run:
name: Clean-up after anatomical run
Expand Down Expand Up @@ -904,7 +908,7 @@ jobs:
--fs-no-reconall --use-syn-sdc --ignore slicetiming \
--dummy-scans 1 --sloppy --write-graph \
--output-spaces MNI152NLin2009cAsym \
--mem_mb 4096 --nthreads 2 -vv
--mem-mb 14336 --nthreads 4 -vv
- run:
name: Checking outputs of fMRIPrep
command: |
Expand Down
4 changes: 2 additions & 2 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -26,14 +26,14 @@ install_requires =
nipype >= 1.5.1
nitime
nitransforms ~= 21.0.0
niworkflows ~= 1.4.5
niworkflows ~= 1.4.9
numpy
packaging
pandas
psutil >= 5.4
pybids >= 0.12.1
requests
sdcflows ~= 2.0.11
sdcflows ~= 2.0.13
smriprep ~= 0.8.0
tedana ~= 0.0.9
templateflow >= 0.6
Expand Down