BIDS: Rename regressors -> timeseries

Author: effigies

.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

.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

.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

.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

.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

.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

.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

.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

docs/outputs.rst

@@ -177,8 +177,8 @@ 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 +233,7 @@ 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 +386,7 @@ 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.

fmriprep/utils/bids.py

@@ -14,7 +14,7 @@ def write_bidsignore(deriv_dir):
         "*.surf.gii",  # Unspecified structural outputs
         # Unspecified functional outputs
         "*_boldref.nii.gz", "*_bold.func.gii",
-        "*_mixing.tsv", "*_AROMAnoiseICs.csv", "*_regressors.tsv",
+        "*_mixing.tsv", "*_AROMAnoiseICs.csv", "*_timeseries.tsv",
     )
     ignore_file = Path(deriv_dir) / ".bidsignore"