Merge branch 'develop' of https://github.com/FCP-INDI/C-PAC into develop

HechengJin0 · HechengJin0 · commit 57181317da8f · 2020-10-20T16:52:02.000-04:00
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -141,11 +141,17 @@ jobs:
               VERSION=$(python -c "from info import __version__; print(__version__)")
               cd ..
               if ! [[ $CIRCLE_BRANCH = 'master' ]]
-                then if [[ $CIRCLE_BRANCH = 'develop' || ${CIRCLE_BRANCH:0:7} = 'hotfix/' ]]
-                  then REBASE_BASE_BRANCH=master
-                  else REBASE_BASE_BRANCH=develop
-                fi
-                GIT_SEQUENCE_EDITOR=dev/circleci_data/drop_version_bump_commits git rebase -X ours -i origin/$REBASE_BASE_BRANCH --empty drop
+                then
+                  git fetch --all
+                  if [[ -n ${CIRCLE_PR_NUMBER} && -n ${GITHUB_PR_BASE_TOKEN} ]]
+                    then
+                      curl -L "https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux64" -o jq
+                      chmod +x jq
+                      REBASE_BASE=origin/$(curl -u shnizzedy:$GITHUB_PR_BASE_TOKEN "https://api.github.com/repos/$CIRCLE_PROJECT_USERNAME/$CIRCLE_PROJECT_REPONAME/pulls/$CIRCLE_PR_NUMBER" | jq '.base.ref' | tr -d '"')
+                  else
+                    REBASE_BASE=$(git rev-parse --short HEAD~30)
+                  fi
+                GIT_SEQUENCE_EDITOR=dev/circleci_data/drop_version_bump_commits git rebase -X ours -i $REBASE_BASE --empty drop
               fi
               echo "v${VERSION}" > version
               sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" dev/docker_data/default_pipeline.yml
diff --git a/CPAC/func_preproc/func_preproc.py b/CPAC/func_preproc/func_preproc.py
diff --git a/CPAC/info.py b/CPAC/info.py
@@ -10,7 +10,7 @@
 # version
 _version_major = 1
 _version_minor = 7
-_version_micro = 0
+_version_micro = 1
 _version_extra = ''
 
 
diff --git a/CPAC/resources/configs/data_config_S3-BIDS-ABIDE.yml b/CPAC/resources/configs/data_config_S3-BIDS-ABIDE.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/data_config_S3-BIDS-ADHD200.yml b/CPAC/resources/configs/data_config_S3-BIDS-ADHD200.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/data_config_S3-BIDS-ADHD200_only2.yml b/CPAC/resources/configs/data_config_S3-BIDS-ADHD200_only2.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/data_config_S3-BIDS-NKI-RocklandSample.yml b/CPAC/resources/configs/data_config_S3-BIDS-NKI-RocklandSample.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/data_config_cpac_benchmark.yml b/CPAC/resources/configs/data_config_cpac_benchmark.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/data_settings_template.yml b/CPAC/resources/configs/data_settings_template.yml
@@ -1,5 +1,5 @@
 # CPAC Data Settings File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/group_config_template.yml b/CPAC/resources/configs/group_config_template.yml
@@ -1,5 +1,5 @@
 # CPAC Group-Level Analysis Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_anat-only.yml b/CPAC/resources/configs/pipeline_config_anat-only.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml b/CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml b/CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_fmriprep-options.yml b/CPAC/resources/configs/pipeline_config_fmriprep-options.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_monkey.yml b/CPAC/resources/configs/pipeline_config_monkey.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_ndmg.yml b/CPAC/resources/configs/pipeline_config_ndmg.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_nhp-macaque.yml b/CPAC/resources/configs/pipeline_config_nhp-macaque.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_preproc.yml b/CPAC/resources/configs/pipeline_config_preproc.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_regtest-1.yml b/CPAC/resources/configs/pipeline_config_regtest-1.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_regtest-2.yml b/CPAC/resources/configs/pipeline_config_regtest-2.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_regtest-3.yml b/CPAC/resources/configs/pipeline_config_regtest-3.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_regtest-4.yml b/CPAC/resources/configs/pipeline_config_regtest-4.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/pipeline_config_rodent.yml b/CPAC/resources/configs/pipeline_config_rodent.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/data-test_S3-ADHD200_1.yml b/CPAC/resources/configs/test_configs/data-test_S3-ADHD200_1.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/data-test_S3-ADHD200_no-params.yml b/CPAC/resources/configs/test_configs/data-test_S3-ADHD200_no-params.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/data-test_S3-NKI-RS_fmap.yml b/CPAC/resources/configs/test_configs/data-test_S3-NKI-RS_fmap.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/data_config_S3_CoRR_5only_mult-scan.yml b/CPAC/resources/configs/test_configs/data_config_S3_CoRR_5only_mult-scan.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/data_config_S3_CoRR_5only_mult-sess.yml b/CPAC/resources/configs/test_configs/data_config_S3_CoRR_5only_mult-sess.yml
@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-AllNuis.yml b/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-AllNuis.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-DistCorr3dSk.yml b/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-DistCorr3dSk.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-DistCorrBET.yml b/CPAC/resources/configs/test_configs/pipe-test_ANTs-3dSk-DistCorrBET.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_ANTs-BET-AllNuis.yml b/CPAC/resources/configs/test_configs/pipe-test_ANTs-BET-AllNuis.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-3dSk-AllNuis.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-3dSk-AllNuis.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-BASC.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-BASC.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-ISC-voxel.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-ISC-voxel.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-ISC.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-ISC.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-MDMR.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis-MDMR.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis.yml b/CPAC/resources/configs/test_configs/pipe-test_FNIRT-BET-AllNuis.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/configs/test_configs/pipe-test_all.yml b/CPAC/resources/configs/test_configs/pipe-test_all.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
diff --git a/CPAC/resources/cpac_outputs.csv b/CPAC/resources/cpac_outputs.csv
@@ -10,7 +10,7 @@ anatomical_brain,anatomical,raw,,,,,,,,,,,,
 anatomical_brain_mask,anatomical,binary,,,,,,,,,,,yes,
 anatomical_csf_mask,anatomical,binary,,,,,,,,,,,,
 anatomical_gm_mask,anatomical,binary,,,,,,,,,,,,
-anatomical_reorient,anatomical,raw,,,,,,,,,,,,
+anat_skull_leaf,anatomical,raw,,,,,,,,,,,,
 mni_to_anatomical_linear_xfm,,transform,,,,,,,,,,,,
 anatomical_to_mni_nonlinear_xfm,,transform,,,,,,,,,,,,
 anatomical_to_standard,template,raw,,,,,,,,,,,,
diff --git a/CPAC/utils/strategy.py b/CPAC/utils/strategy.py
@@ -148,6 +148,8 @@ def get_forking_labels(strategies):
                     fork_label += '_func-3dvolreg'     
                 if 'anat_refined' in fork:
                     fork_label = 'func-anat-refined' 
+                if 'motion_filter' in fork:
+                    fork_label = 'motion-filter'
                 # distortion correction
                 if 'epi_distcorr' in fork:
                     fork_label = 'dist-corr'
@@ -162,7 +164,9 @@ def get_forking_labels(strategies):
                     fork_label = 'freq-filter'
                 
                 if 'gen_motion_stats_before_stc' in fork:
-                    fork_label = 'motion_stats_before_stc' 
+                    fork_label = 'motion_stats_before_stc'
+                if 'despike' in fork:
+                    fork_label = 'despike'
                 if 'slice' in fork:
                     fork_label = 'slice'
                 if 'anat_preproc_afni' in fork:
diff --git a/dev/docker_data/default_pipeline.yml b/dev/docker_data/default_pipeline.yml
@@ -1,5 +1,5 @@
 # CPAC Pipeline Configuration YAML file
-# Version 1.7.0
+# Version 1.7.1
 #
 # http://fcp-indi.github.io for more info.
 #
@@ -678,7 +678,9 @@ functional_volreg_twopass :  On
 #     https://www.biorxiv.org/content/10.1101/337360v1.full.pdf
 motion_estimate_filter:
 
-    run: False
+    # run: [On, Off]
+    # this is a fork option
+    run: [Off]
 
     # options: "notch", "lowpass"
     filter_type: "notch"
diff --git a/version b/version
@@ -1 +1 @@
-v1.7.0
+v1.7.1

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# CPAC Data Configuration File`
`2`		`-# Version 1.7.0`
	`2`	`+# Version 1.7.1`
`3`	`3`	`#`
`4`	`4`	`# http://fcp-indi.github.io for more info.`
`5`	`5`	`#`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# CPAC Data Settings File`
`2`		`-# Version 1.7.0`
	`2`	`+# Version 1.7.1`
`3`	`3`	`#`
`4`	`4`	`# http://fcp-indi.github.io for more info.`
`5`	`5`	`#`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# CPAC Group-Level Analysis Configuration YAML file`
`2`		`-# Version 1.7.0`
	`2`	`+# Version 1.7.1`
`3`	`3`	`#`
`4`	`4`	`# http://fcp-indi.github.io for more info.`
`5`	`5`	`#`