Merge pull request #2223 from effigies/enh/derivatives

effigies · web-flow · commit 1830b255a45c · 2020-09-01T14:19:39.000-04:00
ENH: Conform to BIDS Derivatives as of BIDS 1.4.0
diff --git a/.circleci/ds005_fasttrack_outputs.txt b/.circleci/ds005_fasttrack_outputs.txt
@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/desc-aparcaseg_dseg.tsv
 fmriprep/desc-aseg_dseg.tsv
@@ -10,8 +11,8 @@ fmriprep/logs/CITATION.tex
 fmriprep/sub-01
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_from-T1w_to-scanner_mode-image_xfm.txt
@@ -44,8 +45,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-brain_mas
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-preproc_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-preproc_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-T1w_to-scanner_mode-image_xfm.txt
diff --git a/.circleci/ds005_outputs.txt b/.circleci/ds005_outputs.txt
@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/desc-aparcaseg_dseg.tsv
 fmriprep/desc-aseg_dseg.tsv
@@ -51,8 +52,8 @@ 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-1_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_from-T1w_to-scanner_mode-image_xfm.txt
@@ -85,8 +86,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-brain_mas
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-preproc_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-T1w_desc-preproc_bold.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-T1w_to-scanner_mode-image_xfm.txt
diff --git a/.circleci/ds005_partial_fasttrack_outputs.txt b/.circleci/ds005_partial_fasttrack_outputs.txt
@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/desc-aparcaseg_dseg.tsv
 fmriprep/desc-aseg_dseg.tsv
@@ -10,8 +11,8 @@ fmriprep/logs/CITATION.tex
 fmriprep/sub-01
 fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_AROMAnoiseICs.csv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-2_from-T1w_to-scanner_mode-image_xfm.txt
diff --git a/.circleci/ds005_partial_outputs.txt b/.circleci/ds005_partial_outputs.txt
@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/desc-aparcaseg_dseg.tsv
 fmriprep/desc-aseg_dseg.tsv
@@ -51,8 +52,8 @@ 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_desc-confounds_regressors.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
diff --git a/.circleci/ds054_fasttrack_outputs.txt b/.circleci/ds054_fasttrack_outputs.txt
@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/logs
 fmriprep/logs/CITATION.bib
@@ -10,8 +11,8 @@ fmriprep/sub-100185/func
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-brain_mask.nii.gz
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_regressors.json
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_timeseries.json
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-preproc_bold.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_from-scanner_to-T1w_mode-image_xfm.txt
@@ -29,8 +30,8 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-T1w_desc-prepro
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-brain_mask.nii.gz
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_regressors.json
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_timeseries.json
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-preproc_bold.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_from-scanner_to-T1w_mode-image_xfm.txt
diff --git a/.circleci/ds054_outputs.txt b/.circleci/ds054_outputs.txt
@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/logs
 fmriprep/logs/CITATION.bib
@@ -29,8 +30,8 @@ fmriprep/sub-100185/func
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-brain_mask.nii.gz
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_regressors.json
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_timeseries.json
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_desc-preproc_bold.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_from-scanner_to-T1w_mode-image_xfm.txt
@@ -48,8 +49,8 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-1_space-T1w_desc-prepro
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_boldref.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-brain_mask.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-brain_mask.nii.gz
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_regressors.json
-fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_regressors.tsv
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_timeseries.json
+fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-confounds_timeseries.tsv
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-preproc_bold.json
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_desc-preproc_bold.nii.gz
 fmriprep/sub-100185/func/sub-100185_task-machinegame_run-2_from-scanner_to-T1w_mode-image_xfm.txt
diff --git a/.circleci/ds210_fasttrack_outputs.txt b/.circleci/ds210_fasttrack_outputs.txt
@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/logs
 fmriprep/logs/CITATION.bib
@@ -7,8 +8,8 @@ fmriprep/logs/CITATION.md
 fmriprep/logs/CITATION.tex
 fmriprep/sub-02
 fmriprep/sub-02/func
-fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_regressors.json
-fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.json
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz
diff --git a/.circleci/ds210_outputs.txt b/.circleci/ds210_outputs.txt
@@ -1,4 +1,5 @@
 fmriprep
+fmriprep/.bidsignore
 fmriprep/dataset_description.json
 fmriprep/logs
 fmriprep/logs/CITATION.bib
@@ -26,8 +27,8 @@ fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
 fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
 fmriprep/sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
 fmriprep/sub-02/func
-fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_regressors.json
-fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_regressors.tsv
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.json
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_desc-confounds_timeseries.tsv
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_from-T1w_to-scanner_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-1_space-MNI152NLin2009cAsym_boldref.nii.gz
diff --git a/docs/links.rst b/docs/links.rst
@@ -1,7 +1,8 @@
 .. _Nipype: http://nipype.readthedocs.io/en/latest/
 .. _BIDS: http://bids.neuroimaging.io
-.. _`BIDS Derivatives`: https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI
-.. _`BIDS Derivatives RC1`: https://docs.google.com/document/d/17ebopupQxuRwp7U7TFvS6BH03ALJOgGHufxK8ToAvyI
+.. _`BIDS Derivatives`: https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html
+.. _`BEP 011`: https://bids-specification.readthedocs.io/en/bep011/05-derivatives/04-structural-derivatives.html
+.. _`BEP 012`: https://bids-specification.readthedocs.io/en/bep012/05-derivatives/05-functional-derivatives.html
 .. _Installation: installation.html
 .. _workflows: workflows.html
 .. _FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
diff --git a/docs/outputs.rst b/docs/outputs.rst
@@ -6,7 +6,8 @@
 Outputs of *fMRIPrep*
 ---------------------
 *fMRIPrep* outputs conform to the :abbr:`BIDS (brain imaging data structure)`
-Derivatives specification (see `BIDS Derivatives RC1`_).
+Derivatives specification (see `BIDS Derivatives`_, along with the
+upcoming `BEP 011`_ and `BEP 012`_).
 *fMRIPrep* generates three broad classes of outcomes:
 
 1. **Visual QA (quality assessment) reports**:
@@ -46,7 +47,7 @@ Derivatives of *fMRIPrep* (preprocessed data)
 ---------------------------------------------
 Preprocessed, or derivative, data are written to
 ``<output dir>/fmriprep/sub-<subject_label>/``.
-The `BIDS Derivatives RC1`_ specification describes the naming and metadata conventions we follow.
+The `BIDS Derivatives`_ specification describes the naming and metadata conventions we follow.
 
 Anatomical derivatives
 ~~~~~~~~~~~~~~~~~~~~~~
@@ -146,7 +147,7 @@ mid-thickness surface mesh::
     func/
       sub-<subject_label>_[specifiers]_space-T1w_desc-aparcaseg_dseg.nii.gz
       sub-<subject_label>_[specifiers]_space-T1w_desc-aseg_dseg.nii.gz
-      sub-<subject_label>_[specifiers]_space-<space_label>_hemi-[LR].func.gii
+      sub-<subject_label>_[specifiers]_space-<space_label>_hemi-[LR]_bold.func.gii
 
 Surface output spaces include ``fsnative`` (full density subject-specific mesh),
 ``fsaverage`` and the down-sampled meshes ``fsaverage6`` (41k vertices) and
@@ -177,8 +178,8 @@ Confounds_ are saved as a :abbr:`TSV (tab-separated value)` file::
 
   sub-<subject_label>/
     func/
-      sub-<subject_label>_[specifiers]_desc-confounds_regressors.tsv
-      sub-<subject_label>_[specifiers]_desc-confounds_regressors.json
+      sub-<subject_label>_[specifiers]_desc-confounds_timeseries.tsv
+      sub-<subject_label>_[specifiers]_desc-confounds_timeseries.json
 
 These :abbr:`TSV (tab-separated values)` tables look like the example below,
 where each row of the file corresponds to one time point found in the
@@ -233,7 +234,7 @@ session and run in :abbr:`TSV (tab-separated value)` files - one column for each
 Such tabular files may include over 100 columns of potential confound regressors.
 
 .. danger::
-   Do not include all columns of ``~_desc-confounds_regressors.tsv`` table
+   Do not include all columns of ``~_desc-confounds_timeseries.tsv`` table
    into your design matrix or denoising procedure.
    Filter the table first, to include only the confounds (or components thereof)
    you want to remove from your fMRI signal.
@@ -386,7 +387,7 @@ For CompCor decompositions, entries include:
   - ``VarianceExplained``: the fraction of variance explained by the component across the decomposition ROI mask.
   - ``CumulativeVarianceExplained``: the total fraction of variance explained by this particular component
     and all preceding components.
-  - ``Retained``: Indicates whether the component was saved in ``desc-confounds_regressors.tsv``
+  - ``Retained``: Indicates whether the component was saved in ``desc-confounds_timeseries.tsv``
     for use in denoising.
     Entries that are not saved in the data file for denoising are still stored in metadata with the
     ``dropped`` prefix.
diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
@@ -12,7 +12,7 @@ def main():
     import gc
     from multiprocessing import Process, Manager
     from .parser import parse_args
-    from ..utils.bids import write_derivative_description
+    from ..utils.bids import write_derivative_description, write_bidsignore
 
     parse_args()
 
@@ -166,6 +166,7 @@ def main():
         write_derivative_description(
             config.execution.bids_dir, config.execution.output_dir / "fmriprep"
         )
+        write_bidsignore(config.execution.output_dir / "fmriprep")
 
         if failed_reports and not config.execution.notrack:
             sentry_sdk.capture_message(
diff --git a/fmriprep/utils/bids.py b/fmriprep/utils/bids.py
@@ -7,20 +7,34 @@
 from pathlib import Path
 
 
+def write_bidsignore(deriv_dir):
+    bids_ignore = (
+        "*.html", "logs/", "figures/",  # Reports
+        "*_xfm.*",  # Unspecified transform files
+        "*.surf.gii",  # Unspecified structural outputs
+        # Unspecified functional outputs
+        "*_boldref.nii.gz", "*_bold.func.gii",
+        "*_mixing.tsv", "*_AROMAnoiseICs.csv", "*_timeseries.tsv",
+    )
+    ignore_file = Path(deriv_dir) / ".bidsignore"
+
+    ignore_file.write_text("\n".join(bids_ignore) + "\n")
+
+
 def write_derivative_description(bids_dir, deriv_dir):
-    from ..__about__ import __version__, __url__, DOWNLOAD_URL
+    from ..__about__ import __version__, DOWNLOAD_URL
 
     bids_dir = Path(bids_dir)
     deriv_dir = Path(deriv_dir)
     desc = {
         'Name': 'fMRIPrep - fMRI PREProcessing workflow',
-        'BIDSVersion': '1.1.1',
-        'PipelineDescription': {
+        'BIDSVersion': '1.4.0',
+        'DatasetType': 'derivative',
+        'GeneratedBy': [{
             'Name': 'fMRIPrep',
             'Version': __version__,
             'CodeURL': DOWNLOAD_URL,
-        },
-        'CodeURL': __url__,
+        }],
         'HowToAcknowledge':
             'Please cite our paper (https://doi.org/10.1038/s41592-018-0235-4), '
             'and include the generated citation boilerplate within the Methods '
@@ -29,30 +43,31 @@ def write_derivative_description(bids_dir, deriv_dir):
 
     # Keys that can only be set by environment
     if 'FMRIPREP_DOCKER_TAG' in os.environ:
-        desc['DockerHubContainerTag'] = os.environ['FMRIPREP_DOCKER_TAG']
+        desc['GeneratedBy'][0]['Container'] = {
+            "Type": "docker",
+            "Tag": f"poldracklab/fmriprep:{os.environ['FMRIPREP_DOCKER_TAG']}"
+        }
     if 'FMRIPREP_SINGULARITY_URL' in os.environ:
-        singularity_url = os.environ['FMRIPREP_SINGULARITY_URL']
-        desc['SingularityContainerURL'] = singularity_url
-
-        singularity_md5 = _get_shub_version(singularity_url)
-        if singularity_md5 and singularity_md5 is not NotImplemented:
-            desc['SingularityContainerMD5'] = _get_shub_version(singularity_url)
+        desc['GeneratedBy'][0]['Container'] = {
+            "Type": "singularity",
+            "URI": os.getenv('FMRIPREP_SINGULARITY_URL')
+        }
 
     # Keys deriving from source dataset
     orig_desc = {}
     fname = bids_dir / 'dataset_description.json'
     if fname.exists():
-        with fname.open() as fobj:
-            orig_desc = json.load(fobj)
+        orig_desc = json.loads(fname.read_text())
 
     if 'DatasetDOI' in orig_desc:
-        desc['SourceDatasetsURLs'] = ['https://doi.org/{}'.format(
-            orig_desc['DatasetDOI'])]
+        desc['SourceDatasets'] = [{
+            'URL': f'https://doi.org/{orig_desc["DatasetDOI"]}',
+            'DOI': orig_desc['DatasetDOI']
+        }]
     if 'License' in orig_desc:
         desc['License'] = orig_desc['License']
 
-    with (deriv_dir / 'dataset_description.json').open('w') as fobj:
-        json.dump(desc, fobj, indent=4)
+    Path.write_text(deriv_dir / 'dataset_description.json', json.dumps(desc, indent=4))
 
 
 def validate_input_dir(exec_env, bids_dir, participant_label):
@@ -140,7 +155,3 @@ def validate_input_dir(exec_env, bids_dir, participant_label):
             subprocess.check_call(['bids-validator', bids_dir, '-c', temp.name])
         except FileNotFoundError:
             print("bids-validator does not appear to be installed", file=sys.stderr)
-
-
-def _get_shub_version(singularity_url):
-    return NotImplemented
diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
@@ -69,7 +69,7 @@ def init_func_derivatives_wf(
     raw_sources.inputs.bids_root = bids_root
 
     ds_confounds = pe.Node(DerivativesDataSink(
-        base_directory=output_dir, desc='confounds', suffix='regressors',
+        base_directory=output_dir, desc='confounds', suffix='timeseries',
         dismiss_entities=("echo",)),
         name="ds_confounds", run_without_submitting=True,
         mem_gb=DEFAULT_MEMORY_MIN_GB)
