CI: Test FreeSurfer subjects directory outside of output directory

Author: effigies

.circleci/config.yml

@@ -113,8 +113,9 @@ jobs:
     steps:
       - restore_cache:
           keys:
-            - data-v6-{{ .Revision }}
-            - data-v6-
+            - data-v7-{{ .Branch }}-{{ .Revision }}
+            - data-v7-{{ .Branch }}
+            - data-v7-
       - run:
           name: Get test data from ds000005
           command: |
@@ -149,11 +150,11 @@ jobs:
       - run:
           name: Get FreeSurfer derivatives for ds000005
           command: |
-            if [[ ! -d /tmp/ds005/derivatives/freesurfer ]]; then
-              mkdir -p /tmp/ds005/derivatives
+            if [[ ! -d /tmp/ds005/freesurfer ]]; then
+              mkdir -p /tmp/ds005
               wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
                 -O ds005_derivatives_freesurfer.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/58fe59eb594d900250960180"
-              tar xvzf ds005_derivatives_freesurfer.tar.gz -C /tmp/ds005/derivatives
+              tar xvzf ds005_derivatives_freesurfer.tar.gz -C /tmp/ds005
             else
               echo "FreeSurfer derivatives of ds000005 were cached"
             fi
@@ -180,10 +181,10 @@ jobs:
             - ds054/nipype.cfg
             - ds210/nipype.cfg
       - save_cache:
-         key: data-v6-{{ .Revision }}-{{ epoch }}
+         key: data-v7-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
          paths:
             - /tmp/data
-            - /tmp/ds005/derivatives/freesurfer
+            - /tmp/ds005/freesurfer
 
   test_pytest:
     machine:
@@ -325,13 +326,13 @@ jobs:
             - docker-v3-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
-            - data-v6-{{ .Revision }}
+            - data-v7-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
-            - ds005-anat-v16-{{ .Branch }}-{{ .Revision }}
-            - ds005-anat-v16-{{ .Branch }}
-            - ds005-anat-v16-master
-            - ds005-anat-v16-
+            - ds005-anat-v17-{{ .Branch }}-{{ .Revision }}
+            - ds005-anat-v17-{{ .Branch }}
+            - ds005-anat-v17-master
+            - ds005-anat-v17-
       - run:
           name: Setting up test
           command: |
@@ -362,6 +363,7 @@ jobs:
                 -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
+                --fs-subjects-dir /tmp/ds005/freesurfer \
                 --skull-strip-template OASIS30ANTs:res-1 \
                 --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \
                 --sloppy --write-graph --mem_mb 4096 \
@@ -373,7 +375,7 @@ jobs:
             rm -rf /tmp/ds005/work/reportlets
             rm -rf /tmp/ds005/derivatives/fmriprep
       - save_cache:
-         key: ds005-anat-v16-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
+         key: ds005-anat-v17-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
          paths:
             - /tmp/ds005/work
 
@@ -389,6 +391,7 @@ jobs:
                 -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
+                --fs-subjects-dir /tmp/ds005/freesurfer \
                 --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
                 --use-aroma \
                 --skull-strip-template OASIS30ANTs:res-1 \
@@ -399,7 +402,6 @@ jobs:
           name: Move intermediate results for second run
           command: |
             mkdir -p /tmp/ds005/derivatives_partial
-            sudo mv /tmp/ds005/derivatives/freesurfer /tmp/ds005/derivatives_partial
             sudo cp -a /tmp/ds005/work /tmp/ds005/work_partial
             sudo rm -rf /tmp/ds005/work_partial/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf
       - run:
@@ -418,6 +420,7 @@ jobs:
                 -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work_partial \
                 /tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
+                --fs-subjects-dir /tmp/ds005/freesurfer \
                 --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
                 --output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
                 --aroma-melodic-dimensionality 2 --use-aroma \
@@ -479,7 +482,7 @@ jobs:
             - docker-v3-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
-            - data-v6-{{ .Revision }}
+            - data-v7-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
             - ds054-anat-v14-{{ .Branch }}-{{ .Revision }}
@@ -616,7 +619,7 @@ jobs:
             - docker-v3-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
-            - data-v6-{{ .Revision }}
+            - data-v7-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
             - ds210-anat-v12-{{ .Branch }}-{{ .Revision }}