diff --git a/.circleci/config.yml b/.circleci/config.yml index 079b9760..b9260f23 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -404,16 +404,17 @@ jobs: cp /tmp/data/${DATASET}/dataset_description.json /tmp/data/${DATASET}-t2only cp -r /tmp/data/${DATASET}/sub-01 /tmp/data/${DATASET}-t2only/sub-01 rm -f /tmp/data/${DATASET}-t2only/sub-01/ses-1mo/anat/*_T1w.* + tree /tmp/data/${DATASET}-t2only - run: name: Run nibabies single anatomical workflow no_output_timeout: 1h command: | - mkdir -p /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only + mkdir -p /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only /tmp/${DATASET}/work-t2only nibabies-wrapper docker /tmp/data/${DATASET}-t2only /tmp/${DATASET}/derivatives/nibabies-t2only participant \ -i nipreps/nibabies:dev \ -e NIBABIES_DEV 1 --user $(id -u):$(id -g) \ --network none --notrack \ - --config $PWD/nipype.cfg -w /tmp/${DATASET}/work \ + --config $PWD/nipype.cfg -w /tmp/${DATASET}/work-t2only \ --fs-subjects-dir /tmp/data/${DATASET}/derivatives/infant-freesurfer \ --skull-strip-template UNCInfant:cohort-1 \ --output-spaces MNIInfant:cohort-1 func \