fix(circle): reduce artifacts in circle and update output files to include MNI152NLin6Asym derivatives

Author: oesteban

.circleci/config.yml

@@ -462,14 +462,20 @@ jobs:
             exit $?
       - run:
           name: Clean working directory
-          when: always
+          when: on_success
           command: |
             sudo chown $(id -un):$(id -gn) -R /tmp/ds005
-            find /tmp/ds005/work -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
-                -not -name "*.mat" -not -name "*.lta" -not -name "*.json" -not -name "*.txt" -not -name "*.pklz" -type f -delete
-            find /tmp/ds005/work_partial -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
-                -not -name "*.mat" -not -name "*.lta" -not -name "*.json" -not -name "*.txt" -not -name "*.pklz" -type f -delete
-            # tar cf - work_partial/ | pigz -2 -p 2 > ds005_workdir.tar.gz && sudo rm -fr work work_partial
+            sudo rm -rf /tmp/ds005/work
+            sudo rm -rf /tmp/ds005/work_partial
+      - run:
+          name: Clean working directory
+          when: on_fail
+          command: |
+            sudo chown $(id -un):$(id -gn) -R /tmp/ds005
+            find /tmp/ds005/work \( -name "*.nii.gz" -or -name "*.nii" -or "*.gii" -or "*.h5" \) \
+                -exec sh -c 'rm -f {}; touch {}' \;
+            find /tmp/ds005/work_partial \( -name "*.nii.gz" -or -name "*.nii" -or "*.gii" -or "*.h5" \) \
+                -exec sh -c 'rm -f {}; touch {}' \;
 
       - store_artifacts:
           path: /tmp/ds005
@@ -588,13 +594,18 @@ jobs:
             set -e
             [[ "$RET" -eq "1" ]]
       - run:
-          name: Clean-up work directory
-          when: always
+          name: Clean working directory
+          when: on_success
+          command: |
+            sudo chown $(id -un):$(id -gn) -R /tmp/ds054
+            sudo rm -rf /tmp/ds054/work
+      - run:
+          name: Clean working directory
+          when: on_fail
           command: |
             sudo chown $(id -un):$(id -gn) -R /tmp/ds054
-            find /tmp/ds054/work -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
-                -not -name "*.mat" -not -name "*.lta" -not -name "*.json" -not -name "*.txt" -not -name "*.pklz" -type f -delete
-            # tar cf - work/ | pigz -2 -p 2 > ds054_workdir.tar.gz && sudo rm -fr work
+            find /tmp/ds054/work \( -name "*.nii.gz" -or -name "*.nii" -or "*.gii" -or "*.h5" \) \
+                -exec sh -c 'rm -f {}; touch {}' \;
       - store_artifacts:
           path: /tmp/ds054
 
@@ -686,13 +697,18 @@ jobs:
             diff /tmp/src/fmriprep/.circleci/ds210_outputs.txt /tmp/ds210/test/outputs.out
             exit $?
       - run:
-          name: Clean-up work directory
-          when: always
+          name: Clean working directory
+          when: on_success
+          command: |
+            sudo chown $(id -un):$(id -gn) -R /tmp/ds210
+            sudo rm -rf /tmp/ds210/work
+      - run:
+          name: Clean working directory
+          when: on_fail
           command: |
             sudo chown $(id -un):$(id -gn) -R /tmp/ds210
-            find /tmp/ds210/work -not -name "*.svg" -not -name "*.html" -not -name "*.rst" \
-                -not -name "*.mat" -not -name "*.lta" -not -name "*.json" -not -name "*.txt" -not -name "*.pklz" -type f -delete
-            # tar cf - work/ | pigz -2 -p 2 > ds054_workdir.tar.gz && sudo rm -fr work
+            find /tmp/ds210/work \( -name "*.nii.gz" -or -name "*.nii" -or "*.gii" -or "*.h5" \) \
+                -exec sh -c 'rm -f {}; touch {}' \;
       - store_artifacts:
           path: /tmp/ds210
 

.circleci/ds005_outputs.txt

@@ -17,9 +17,11 @@ fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.json
 fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
 fmriprep/sub-01/anat/sub-01_dseg.nii.gz
 fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
+fmriprep/sub-01/anat/sub-01_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
 fmriprep/sub-01/anat/sub-01_from-orig_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
+fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
 fmriprep/sub-01/anat/sub-01_hemi-L_inflated.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
@@ -39,6 +41,14 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-brain_mask.json
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-preproc_T1w.json
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_dseg.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.dtseries.json
@@ -57,6 +67,14 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAs
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_boldref.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-aparcaseg_dseg.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-aseg_dseg.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-brain_mask.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-preproc_bold.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aparcaseg_dseg.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aseg_dseg.nii.gz
@@ -81,6 +99,14 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAs
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_boldref.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-aparcaseg_dseg.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-aseg_dseg.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aparcaseg_dseg.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aseg_dseg.nii.gz

.circleci/ds005_partial_outputs.txt

@@ -17,9 +17,11 @@ fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.json
 fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
 fmriprep/sub-01/anat/sub-01_dseg.nii.gz
 fmriprep/sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
+fmriprep/sub-01/anat/sub-01_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
 fmriprep/sub-01/anat/sub-01_from-orig_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
+fmriprep/sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
 fmriprep/sub-01/anat/sub-01_hemi-L_inflated.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
 fmriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
@@ -39,6 +41,14 @@ fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
 fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-brain_mask.json
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-preproc_T1w.json
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_dseg.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
+fmriprep/sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.json
@@ -57,6 +67,14 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAs
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_boldref.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-aparcaseg_dseg.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-aseg_dseg.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aparcaseg_dseg.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aseg_dseg.nii.gz