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Merge remote-tracking branch 'upstream/master' into fix-stc
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‎.circleci/config.yml

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at: /tmp
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- restore_cache:
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keys:
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- ds005-anat-v9-{{ .Branch }}-{{ epoch }}
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- ds005-anat-v9-{{ .Branch }}
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- ds005-anat-v9-master
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- ds005-anat-v9-
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- ds005-anat-v10-{{ .Branch }}-{{ epoch }}
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- ds005-anat-v10-{{ .Branch }}
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- ds005-anat-v10-master
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- ds005-anat-v10-
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- run:
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name: Setting up test
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command: |
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--sloppy --write-graph --mem_mb 4096 \
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--nthreads 2 --anat-only -vv
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- save_cache:
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key: ds005-anat-v9-{{ .Branch }}-{{ epoch }}
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key: ds005-anat-v10-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds005/work
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- /tmp/ds005/derivatives/fmriprep
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at: /tmp
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- restore_cache:
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keys:
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- ds210-anat-v4-{{ epoch }}
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- ds210-anat-v4-
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- ds210-anat-v5-{{ .Branch }}-{{ epoch }}
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- ds210-anat-v5-{{ .Branch }}
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- ds210-anat-v5-master
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- ds210-anat-v5-
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- run:
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name: Setting up test
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command: |
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--fs-no-reconall --sloppy --write-graph \
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--mem_mb 4096 --nthreads 2 --anat-only -vv
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- save_cache:
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key: ds210-anat-v4-{{ epoch }}
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key: ds210-anat-v5-{{ .Branch }}-{{ epoch }}
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paths:
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- /tmp/ds210/work
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- /tmp/ds210/derivatives
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- /ds005\/.*/
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- /ds054\/.*/
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- /ds210\/.*/
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tags:
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only: /.*/
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- build_docs:
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requires:
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- get_regression_data
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filters:
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branches:
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ignore:
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ignore:
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- /docs?\/.*/
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- /ds005\/.*/
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- /ds054\/.*/

‎.circleci/ds005_outputs.txt

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@@ -6,6 +6,8 @@ fmriprep/logs/CITATION.md
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fmriprep/logs/CITATION.tex
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fmriprep/sub-01
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fmriprep/sub-01/anat
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fmriprep/sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
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fmriprep/sub-01/anat/sub-01_label-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-aseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz
@@ -45,10 +45,10 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAs
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.nii
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_label-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_label-aseg_dseg.nii.gz
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fmriprep/sub-01.html
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/tmp/ds005/derivatives

‎.circleci/ds005_partial_outputs.txt

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fmriprep/logs/CITATION.tex
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fmriprep/sub-01
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fmriprep/sub-01/anat
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fmriprep/sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
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fmriprep/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
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fmriprep/sub-01/anat/sub-01_label-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-aseg_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
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fmriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_desc-preproc_bold.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aseg_dseg.nii.gz
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fmriprep/sub-01.html
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/tmp/ds005/derivatives_partial

‎CHANGES.rst

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1.2.1 (November 1, 2018)
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========================
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Hotfix release (deployment system)
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1.2.0 (October 31, 2018)
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========================
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This release marks a substantial renaming of derivatives to conform to the BIDS Derivatives specification [release candidate](https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI/).
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The most significant additional change is a substantial revision of BOLD skull-stripping, using a BOLD template constructed from many open datasets. Building off the work of Zhifang Ye (see #1050), the skull-stripping is now much more resilient to intensity inhomogeneity.
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With many thanks to Ali Cohen, James Kent, Inge Amlien, Sebastian Urchs, and Zhifang Ye for contributions.
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* [FIX] Missing BOLD reports (#1326) @oesteban
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* [FIX] Ensure encoding when reading boilerplate (#1322) @alioco
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* [FIX] Reportlets - bbregister vs flirtbbr (continues #1326) (#1328) @oesteban
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* [FIX] Quick update to new template structure (#1330) @oesteban
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* [FIX] Explicitly pass bold mask to AROMA (#1332) @jdkent
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* [FIX] Missing report output - #1339 (#1346) @kasbohm
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* [FIX] Remove non-steady-state volumes prior to ICA-AROMA (#1335) @jdkent
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* [ENH] Store BOLD reference images (#1306) @oesteban
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* [ENH] Deprecate --debug with --sloppy (#1347) @effigies
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* [ENH] Conform confound regressor names to Derivatives RC2 (#1343) @effigies
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* [ENH] Do not set KEEP_FILE_OPEN_DEFAULT (#1356) @effigies
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* [ENH] Template-based masking of EPI boldrefs (#1321) @oesteban
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* [DOC] Update BIDS-validator link (#1320) @surchs
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* [DOC] add --bind method to singularity patch documentation (#1340) @jdkent
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* [RF] Update anatomical derivatives for RC1 (#1325) @effigies
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* [RF] Update functional derivatives for RC1 (#1333) @effigies
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* [TST] Add heavily-nonuniform boldrefs for regression tests (#1329) @oesteban
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* [TST] Fix expectations for CIFTI outputs & ds005 (#1344) @oesteban
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* [MAINT] Ignore project settings files from popular python/code editors (#1336) @jdkent
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* [CI] Deploy poldracklab/fmriprep:unstable tracking master (#1307) @effigies
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1.1.8 (October 4, 2018)
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=======================
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‎docs/citing.rst

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.. [Power2017] Power JD, Plitt M, Kundu P, Bandettini PA, Martin A (2017) Temporal interpolation alters
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motion in fMRI scans: Magnitudes and consequences for artifact detection. PLOS ONE 12(9): e0182939.
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doi:`10.1371/journal.pone.0182939 <https://doi.org/10.1371/journal.pone.0182939>`_.
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.. [Brett2001] Brett M, Leff AP, Rorden C, Ashburner J (2001) Spatial Normalization of Brain Images with
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Focal Lesions Using Cost Function Masking. NeuroImage 14(2)
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.. [Brett2001] Brett M, Leff AP, Rorden C, Ashburner J (2001) Spatial Normalization of Brain Images with
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Focal Lesions Using Cost Function Masking. NeuroImage 14(2)
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doi:`10.006/nimg.2001.0845 <https://doi.org/10.1006/nimg.2001.0845>`_.

‎docs/links.rst

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.. _Nipype: http://nipype.readthedocs.io/en/latest/
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.. _BIDS: http://bids.neuroimaging.io
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.. _`BIDS Derivatives`: https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/edit
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.. _`BIDS Derivatives`: https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI
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.. _`BIDS Derivatives RC1`: https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI
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.. _Usage: usage.html
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.. _Installation: installation.html
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.. _workflows: workflows.html

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