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Merge pull request #1546 from oesteban/enh/write-deriv-metadata
ENH: Write derivatives metadata
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‎.circleci/ds005_outputs.txt

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fmriprep
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fmriprep/dataset_description.json
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fmriprep/desc-aparcaseg_dseg.tsv
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fmriprep/desc-aseg_dseg.tsv
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fmriprep/logs
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fmriprep/logs/CITATION.bib
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fmriprep/logs/CITATION.html
@@ -9,7 +11,9 @@ 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.json
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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.json
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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_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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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/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
@@ -46,13 +52,17 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsnative_hemi-R.f
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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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.json
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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.json
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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-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_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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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.json
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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.json
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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.html
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/tmp/ds005/derivatives

‎.circleci/ds005_partial_outputs.txt

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fmriprep
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fmriprep/dataset_description.json
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fmriprep/desc-aparcaseg_dseg.tsv
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fmriprep/desc-aseg_dseg.tsv
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fmriprep/logs
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fmriprep/logs/CITATION.bib
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fmriprep/logs/CITATION.html
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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.json
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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.json
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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_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
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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/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
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fmriprep/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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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.json
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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.json
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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.html
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/tmp/ds005/derivatives_partial

‎.circleci/ds054_outputs.txt

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fmriprep/logs/CITATION.tex
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fmriprep/sub-100185/anat
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fmriprep/sub-100185/anat/sub-100185_desc-brain_mask.json
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fmriprep/sub-100185/anat/sub-100185_desc-brain_mask.nii.gz
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fmriprep/sub-100185/anat/sub-100185_desc-preproc_T1w.json
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fmriprep/sub-100185/anat/sub-100185_desc-preproc_T1w.nii.gz
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fmriprep/sub-100185/anat/sub-100185_dseg.nii.gz
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fmriprep/sub-100185/anat/sub-100185_label-CSF_probseg.nii.gz
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fmriprep/sub-100185/anat/sub-100185_label-GM_probseg.nii.gz
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fmriprep/sub-100185/anat/sub-100185_label-WM_probseg.nii.gz
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fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
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fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
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fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
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fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_dseg.nii.gz
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fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
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fmriprep/sub-100185/func
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_regressors.tsv
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_regressors.tsv
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_boldref.nii.gz
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain_mask.json
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fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.json
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/tmp/ds054/derivatives

‎.circleci/ds210_outputs.txt

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fmriprep/sub-02/anat/sub-02_desc-brain_mask.json
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fmriprep/sub-02/anat/sub-02_desc-brain_mask.nii.gz
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fmriprep/sub-02/anat/sub-02_desc-preproc_T1w.json
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fmriprep/sub-02/anat/sub-02_desc-preproc_T1w.nii.gz
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fmriprep/sub-02/anat/sub-02_dseg.nii.gz
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fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
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fmriprep/sub-02/func
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
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fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
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/tmp/ds210/derivatives

‎Dockerfile

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# Precaching atlases
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ENV TEMPLATEFLOW_HOME="/opt/templateflow"
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RUN mkdir -p $TEMPLATEFLOW_HOME
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RUN pip install --no-cache-dir "templateflow>=0.1.0,<0.2.0a0" && \
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RUN pip install --no-cache-dir "templateflow>=0.1.3,<0.2.0a0" && \
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python -c "from templateflow import api as tfapi; \
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tfapi.get('MNI152Lin'); \
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‎docs/environment.yml

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- svgutils
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- nitime
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- nilearn
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- niworkflows>=0.7.2,<0.8.0a0
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- smriprep>=0.0.4,<0.1.0a0
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- niworkflows<0.9.0a0,>=0.8.1
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- smriprep
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- tedana>=0.0.5

‎docs/workflows.rst

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from fmriprep.workflows.anatomical import init_anat_preproc_wf
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wf = init_anat_preproc_wf(omp_nthreads=1,
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reportlets_dir='.',
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output_dir='.',
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template='MNI152NLin2009cAsym',
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fs_spaces=['T1w', 'fsnative',
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'template', 'fsaverage5'],
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skull_strip_template='OASIS30ANTs',
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skull_strip_fixed_seed=False,
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freesurfer=True,
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longitudinal=False,
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debug=False,
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hires=True,
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num_t1w=1)
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wf = init_anat_preproc_wf(
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bids_root='.',
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debug=False,
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freesurfer=True,
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fs_spaces=['T1w', 'fsnative',
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'template', 'fsaverage5'],
75+
hires=True,
76+
longitudinal=False,
77+
num_t1w=1,
78+
omp_nthreads=1,
79+
output_dir='.',
80+
reportlets_dir='.',
81+
skull_strip_template='MNI152NLin2009cAsym',
82+
skull_strip_fixed_seed=False,
83+
template='MNI152NLin2009cAsym',
84+
)
8285

8386
The anatomical sub-workflow begins by constructing an average image by
8487
conforming all found T1w images to RAS orientation and
@@ -90,8 +93,19 @@ single reference template (see `Longitudinal processing`_).
9093
Brain extraction, brain tissue segmentation and spatial normalization
9194
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
9295

93-
Then, the T1w image/average is skull-stripped using ANTs' ``antsBrainExtraction.sh``,
94-
which is an atlas-based brain extraction workflow.
96+
Then, the T1w reference is skull-stripped using a Nipype implementation of
97+
the ``antsBrainExtraction.sh`` tool (ANTs), which is an atlas-based
98+
brain extraction workflow:
99+
100+
.. workflow::
101+
:graph2use: orig
102+
:simple_form: yes
103+
104+
from niworkflows.anat.ants import init_brain_extraction_wf
105+
wf = init_brain_extraction_wf()
106+
107+
108+
An example of brain extraction is shown below:
95109

96110
.. figure:: _static/brainextraction_t1.svg
97111
:scale: 100%
@@ -251,31 +265,34 @@ BOLD preprocessing
251265
:graph2use: orig
252266
:simple_form: yes
253267

268+
from collections import namedtuple
269+
BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
254270
from fmriprep.workflows.bold import init_func_preproc_wf
255271
wf = init_func_preproc_wf(
256272
'/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
257-
omp_nthreads=1,
258-
ignore=[],
259-
freesurfer=True,
260-
reportlets_dir='.',
261-
output_dir='.',
262-
template='MNI152NLin2009cAsym',
263-
output_spaces=['T1w', 'fsnative', 'template', 'fsaverage5'],
264-
medial_surface_nan=False,
273+
aroma_melodic_dim=-200,
274+
bold2t1w_dof=9,
265275
cifti_output=False,
266276
debug=False,
267-
low_mem=False,
268-
use_bbr=True,
269-
t2s_coreg=False,
270-
bold2t1w_dof=9,
277+
err_on_aroma_warn=False,
271278
fmap_bspline=True,
272279
fmap_demean=True,
273-
use_syn=True,
274280
force_syn=True,
281+
freesurfer=True,
282+
ignore=[],
283+
layout=BIDSLayout(),
284+
low_mem=False,
285+
medial_surface_nan=False,
286+
omp_nthreads=1,
287+
output_dir='.',
288+
output_spaces=['T1w', 'fsnative', 'template', 'fsaverage5'],
289+
reportlets_dir='.',
290+
t2s_coreg=False,
291+
template='MNI152NLin2009cAsym',
275292
template_out_grid='native',
276293
use_aroma=False,
277-
aroma_melodic_dim=-200,
278-
err_on_aroma_warn=False,
294+
use_bbr=True,
295+
use_syn=True,
279296
)
280297

281298
Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is

‎fmriprep/__about__.py

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -89,21 +89,23 @@
8989
'nilearn',
9090
'nipype>=1.1.6',
9191
'nitime',
92-
'niworkflows<0.9.0a0,>=0.8.0',
92+
'niworkflows<0.9.0a0,>=0.8.1',
9393
'numpy',
9494
'pandas',
9595
'psutil>=5.4',
9696
'pybids<0.8.0a0,>=0.7.1',
9797
'pyyaml',
9898
'scikit-image',
99-
'smriprep<0.2.0a0,>=0.1.0',
99+
'smriprep',
100100
'statsmodels',
101101
'tedana>=0.0.5',
102-
'templateflow<0.2.0a0,>=0.1.0',
102+
'templateflow<0.2.0a0,>=0.1.3',
103103
]
104104

105105

106106
LINKS_REQUIRES = [
107+
'git+https://github.com/poldracklab/smriprep.git@'
108+
'423bcc43ab7300177eb3b98da62817b2cad8eb87#egg=smriprep-0.1.0',
107109
]
108110

109111
TESTS_REQUIRES = [

‎fmriprep/cli/run.py

Lines changed: 11 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -185,7 +185,7 @@ def get_parser():
185185
# ANTs options
186186
g_ants = parser.add_argument_group('Specific options for ANTs registrations')
187187
g_ants.add_argument('--skull-strip-template', action='store', default='OASIS30ANTs',
188-
choices=['OASIS30ANTs', 'NKI'],
188+
choices=['OASIS30ANTs', 'NKI', 'MNI152NLin2009cAsym'],
189189
help='select ANTs skull-stripping template (default: OASIS30ANTs))')
190190
g_ants.add_argument('--skull-strip-fixed-seed', action='store_true',
191191
help='do not use a random seed for skull-stripping - will ensure '
@@ -439,6 +439,16 @@ def before_send(event, hints):
439439
if "Workflow did not execute cleanly" not in str(e):
440440
sentry_sdk.capture_exception(e)
441441
raise
442+
else:
443+
if opts.run_reconall:
444+
from templateflow import api
445+
from niworkflows.utils.misc import _copy_any
446+
dseg_tsv = str(api.get('fsaverage', suffix='dseg', extensions=['.tsv']))
447+
_copy_any(dseg_tsv,
448+
str(Path(output_dir) / 'fmriprep' / 'desc-aseg_dseg.tsv'))
449+
_copy_any(dseg_tsv,
450+
str(Path(output_dir) / 'fmriprep' / 'desc-aparcaseg_dseg.tsv'))
451+
logger.log(25, 'fMRIPrep finished without errors')
442452
finally:
443453
# Generate reports phase
444454
errno += generate_reports(subject_list, output_dir, work_dir, run_uuid,

‎fmriprep/workflows/anatomical.py

Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,6 @@
66
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
77
88
.. autofunction:: init_anat_preproc_wf
9-
.. autofunction:: init_skullstrip_ants_wf
109
1110
Surface preprocessing
1211
+++++++++++++++++++++
@@ -21,7 +20,6 @@
2120
"""
2221
from smriprep.workflows.anatomical import (
2322
init_anat_preproc_wf,
24-
init_skullstrip_ants_wf,
2523
)
2624
from smriprep.workflows.surfaces import (
2725
init_surface_recon_wf,
@@ -31,7 +29,6 @@
3129

3230
__all__ = [
3331
'init_anat_preproc_wf',
34-
'init_skullstrip_ants_wf',
3532
'init_surface_recon_wf',
3633
'init_autorecon_resume_wf',
3734
'init_gifti_surface_wf',

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