Repository: PennLINC/xcp_d

Issue:
Rename ALFF and ReHo outputs based on BEP 012
## Summary
<!--What would you like changed/added and why?-->
In BEP 012 (see https://github.com/bids-standard/bids-specification/pull/519), they use `_stat-<reho|alff>_boldmap` instead of `_<alff|reho>`.


Discussion:
codecov[bot]: ## [Codecov](https://app.codecov.io/gh/PennLINC/xcp_d/pull/1065?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=PennLINC) Report
All modified and coverable lines are covered by tests :white_check_mark:
> Project coverage is 82.35%. Comparing base [(`b2d16c1`)](https://app.codecov.io/gh/PennLINC/xcp_d/commit/b2d16c17b006cdf756bf0cb0f6b08dcab06e0f1d?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=PennLINC) to head [(`ee52b13`)](https://app.codecov.io/gh/PennLINC/xcp_d/pull/1065?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=PennLINC).

> :exclamation: Current head ee52b13 differs from pull request most recent head a404010. Consider uploading reports for the commit a404010 to get more accurate results


<details><summary>Additional details and impacted files</summary>


```diff
@@            Coverage Diff             @@
##             main    #1065      +/-   ##
==========================================
+ Coverage   82.33%   82.35%   +0.02%     
==========================================
  Files          48       48              
  Lines        5897     5882      -15     
  Branches      796      791       -5     
==========================================
- Hits         4855     4844      -11     
+ Misses        839      836       -3     
+ Partials      203      202       -1     
```



</details>

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tsalo: @mattcieslak @kahinimehta would you mind taking a look at the new filenames some time next week to see if they align with your understanding to the relevant BEPs?

Patch:
diff --git a/docs/outputs.rst b/docs/outputs.rst
index c7984bc..986bcdb 100644
--- a/docs/outputs.rst
+++ b/docs/outputs.rst
@@ -9,23 +9,25 @@ The  *XCP-D* outputs are written out in BIDS format and consist of three main pa
 
 .. admonition:: A note on BIDS compliance
 
-   *XCP-D* attempts to follow the BIDS specification as best as possible.
+   *XCP-D* attempts to follow the BIDS specification as closely as possible.
    However, many *XCP-D* derivatives are not currently covered by the specification.
    In those instances, we attempt to follow recommendations from existing BIDS Extension Proposals
    (BEPs), which are in-progress proposals to add new features to BIDS.
+   However, we do not guarantee compliance with any BEP,
+   as they are not yet part of the official BIDS specification.
 
-   Three BEPs that are of particular use in *XCP-D* are
+   Four BEPs that are of particular use in *XCP-D* are
+   `BEP011: Structural preprocessing derivatives <https://github.com/bids-standard/bids-specification/pull/518>`_,
    `BEP012: Functional preprocessing derivatives <https://github.com/bids-standard/bids-specification/pull/519>`_,
-   `BEP017: BIDS connectivity matrix data schema <https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA/edit?usp=sharing>`_,
+   `BEP017: Relationship & connectivity matrix data schema <https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA/edit?usp=sharing>`_,
    and
-   `BEP038: Atlas Specification <https://docs.google.com/document/d/1RxW4cARr3-EiBEcXjLpSIVidvnUSHE7yJCUY91i5TfM/edit?usp=sharing>`_
-   (currently unnumbered).
+   `BEP038: Atlas Specification <https://docs.google.com/document/d/1RxW4cARr3-EiBEcXjLpSIVidvnUSHE7yJCUY91i5TfM/edit?usp=sharing>`_.
 
    In cases where a derivative type is not covered by an existing BEP,
    we have simply attempted to follow the general principles of BIDS.
 
-   If you discover a problem with the BIDS compliance of *XCP-D*'s derivatives, please open an
-   issue in the *XCP-D* repository.
+   If you discover a problem with the BIDS compliance of *XCP-D*'s derivatives,
+   please open an issue in the *XCP-D* repository.
 
 
 ***************
@@ -86,15 +88,16 @@ Atlases are written out to the ``atlases`` subfolder, following BEP038.
 
    xcp_d/
       atlases/
+         dataset_description.json
          atlas-<label>/
             atlas-<label>_dseg.json
             atlas-<label>_dseg.tsv
 
             # NIfTI
-            space-<label>_atlas-<label>_dseg.nii.gz
+            atlas-<label>_space-<label>_dseg.nii.gz
 
             # CIFTI
-            space-<label>_atlas-<label>_dseg.dlabel.nii
+            atlas-<label>_space-<label>_dseg.dlabel.nii
 
 
 ******************
@@ -155,9 +158,9 @@ atlases it uses to parcellate the functional outputs.
    xcp_d/
       sub-<label>/[ses-<label>/]
          anat/
-            <source_entities>_space-fsLR_atlas-<atlas>_den-32k_desc-curv_morph.tsv
-            <source_entities>_space-fsLR_atlas-<atlas>_den-32k_desc-sulc_morph.tsv
-            <source_entities>_space-fsLR_atlas-<atlas>_den-32k_desc-thickness_morph.tsv
+            <source_entities>_space-fsLR_seg-<label>_den-32k_stat-mean_desc-curv_morph.tsv
+            <source_entities>_space-fsLR_seg-<label>_den-32k_stat-mean_desc-sulc_morph.tsv
+            <source_entities>_space-fsLR_seg-<label>_den-32k_stat-mean_desc-thickness_morph.tsv
 
 
 ******************
@@ -208,15 +211,33 @@ Denoised or residual BOLD data
    and primarily exist for compatibility with DCAN-specific analysis tools.
 
 The sidecar json files contains parameters of the data and processing steps.
+The Sources field contains BIDS URIs pointing to the files used to create the derivative.
+The associated DatasetLinks are defined in the dataset_description.json.
 
    .. code-block:: json-object
 
       {
-         "Freq Band": [0.01, 0.08],
-         "RepetitionTime": 2.0,
-         "compression": true,
-         "dummy vols": 0,
-         "nuisance parameters": "27P",
+         "EchoTime": 0.0424,
+         "EffectiveEchoSpacing": 0.000639989,
+         "FlipAngle": 51,
+         "Manufacturer": "Siemens",
+         "ManufacturersModelName": "Skyra",
+         "NuisanceParameters": "gsr_only",
+         "PhaseEncodingDirection": "j-",
+         "RepetitionTime": 3,
+         "SoftwareFilters": {
+            "Bandpass filter": {
+               "Filter order": 2,
+               "High-pass cutoff (Hz)": 0.01,
+               "Low-pass cutoff (Hz)": 0.08
+            }
+         },
+         "Sources": [
+            "bids:preprocessed:sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz",
+            "bids:xcp_d:sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_outliers.tsv",
+            "bids:xcp_d:sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_desc-preproc_design.tsv"
+         ],
+         "TaskName": "resting state"
       }
 
 
@@ -235,19 +256,19 @@ This includes the atlases used to extract the timeseries.
       sub-<label>/[ses-<label>/]
          func/
             # NIfTI
-            <source_entities>_space-<label>_atlas-<label>_coverage.tsv
-            <source_entities>_space-<label>_atlas-<label>_timeseries.tsv
-            <source_entities>_space-<label>_atlas-<label>_measure-pearsoncorrelation_conmat.tsv
-            <source_entities>_space-<label>_atlas-<label>_measure-pearsoncorrelation_desc-<INT>volumes_conmat.tsv
+            <source_entities>_space-<label>_seg-<label>_stat-coverage_bold.tsv
+            <source_entities>_space-<label>_seg-<label>_stat-mean_timeseries.tsv
+            <source_entities>_space-<label>_seg-<label>_stat-pearsoncorrelation_relmat.tsv
+            <source_entities>_space-<label>_seg-<label>_stat-pearsoncorrelation_desc-<INT>volumes_relmat.tsv
 
             # CIFTI
-            <source_entities>_space-fsLR_atlas-<label>_den-91k_coverage.tsv
-            <source_entities>_space-fsLR_atlas-<label>_den-91k_coverage.pscalar.nii
-            <source_entities>_space-fsLR_atlas-<label>_den-91k_timeseries.tsv
-            <source_entities>_space-fsLR_atlas-<label>_den-91k_timeseries.ptseries.nii
-            <source_entities>_space-fsLR_atlas-<label>_den-91k_measure-pearsoncorrelation_conmat.tsv
-            <source_entities>_space-fsLR_atlas-<label>_den-91k_measure-pearsoncorrelation_conmat.pconn.nii
-            <source_entities>_space-fsLR_atlas-<label>_den-91k_measure-pearsoncorrelation_desc-<INT>volumes_conmat.tsv
+            <source_entities>_space-fsLR_seg-<label>_den-91k_stat-coverage_bold.tsv
+            <source_entities>_space-fsLR_seg-<label>_den-91k_stat-coverage_boldmap.pscalar.nii
+            <source_entities>_space-fsLR_seg-<label>_den-91k_stat-mean_timeseries.tsv
+            <source_entities>_space-fsLR_seg-<label>_den-91k_stat-mean_timeseries.ptseries.nii
+            <source_entities>_space-fsLR_seg-<label>_den-91k_stat-pearsoncorrelation_relmat.tsv
+            <source_entities>_space-fsLR_seg-<label>_den-91k_stat-pearsoncorrelation_boldmap.pconn.nii
+            <source_entities>_space-fsLR_seg-<label>_den-91k_stat-pearsoncorrelation_desc-<INT>volumes_relmat.tsv
 
 
 Resting-state metric derivatives (ReHo and ALFF)
@@ -273,18 +294,18 @@ data.
       sub-<label>/[ses-<label>/]
          func/
             # NIfTI
-            <source_entities>_space-<label>_reho.nii.gz
-            <source_entities>_space-<label>_alff.nii.gz
-            <source_entities>_space-<label>_desc-smooth_alff.nii.gz
-            <source_entities>_space-<label>_atlas-<atlas>_alff.tsv
-            <source_entities>_space-<label>_atlas-<atlas>_reho.tsv
+            <source_entities>_space-<label>_stat-reho_boldmap.nii.gz
+            <source_entities>_space-<label>_stat-alff_boldmap.nii.gz
+            <source_entities>_space-<label>_stat-alff_desc-smooth_boldmap.nii.gz
+            <source_entities>_space-<label>_seg-<label>_stat-alff_bold.tsv
+            <source_entities>_space-<label>_seg-<label>_stat-reho_bold.tsv
 
             # CIFTI
-            <source_entities>_space-fsLR_den-91k_reho.dscalar.nii
-            <source_entities>_space-fsLR_den-91k_alff.dscalar.nii
-            <source_entities>_space-fsLR_den-91k_desc-smooth_alff.dscalar.nii
-            <source_entities>_space-fsLR_atlas-<atlas>_alff.tsv
-            <source_entities>_space-fsLR_atlas-<atlas>_reho.tsv
+            <source_entities>_space-fsLR_den-91k_stat-reho_boldmap.dscalar.nii
+            <source_entities>_space-fsLR_den-91k_stat-alff_boldmap.dscalar.nii
+            <source_entities>_space-fsLR_den-91k_stat-alff_desc-smooth_boldmap.dscalar.nii
+            <source_entities>_space-fsLR_seg-<label>_stat-alff_bold.tsv
+            <source_entities>_space-fsLR_seg-<label>_stat-reho_bold.tsv
 
 
 Other outputs include quality control, framewise displacement, and confounds files
@@ -300,12 +321,7 @@ Other outputs include quality control, framewise displacement, and confounds fil
             <source_entities>[_desc-filtered]_motion.tsv
             <source_entities>_outliers.tsv
             <source_entities>_design.tsv
-
-            # NIfTI
-            <source_entities>_space-<label>_desc-linc_qc.csv
-
-            # CIFTI
-            <source_entities>_space-fsLR_desc-linc_qc.csv
+            <source_entities>_space-<label>_desc-linc_qc.tsv
 
 ``[desc-filtered]_motion.tsv`` is a tab-delimited file with seven columns:
 one for each of the six filtered motion parameters, as well as "framewise_displacement".
diff --git a/docs/usage.rst b/docs/usage.rst
index 86f106b..4b10ae3 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -419,7 +419,7 @@ generate the time series:
       -cifti-parcellate \
       {SUB}_ses-{SESSION}_task-{TASK}_run-{RUN}_space-fsLR_den-91k_desc-residual_bold.dtseries.nii \
       your_parcels.dlabel \
-      {SUB}_ses-{SESSION}_task-{TASK}_run-{RUN}_space-fsLR_den-91k_desc-residual_bold.ptseries.nii
+      {SUB}_ses-{SESSION}_task-{TASK}_run-{RUN}_space-fsLR_den-91k_desc-residual_timeseries.ptseries.nii
 
 After this, if one wishes to have a connectivity matrix:
 
@@ -427,8 +427,8 @@ After this, if one wishes to have a connectivity matrix:
 
    wb_command \
       -cifti-correlation \
-      {SUB}_ses-{SESSION}_task-{TASK}_run-{RUN}_space-fsLR_den-91k_desc-residual_bold.ptseries.nii \
-      {SUB}_ses-{SESSION}_task-{TASK}_run-{RUN}_space-fsLR_den-91k_desc-residual_bold.pconn.nii
+      {SUB}_ses-{SESSION}_task-{TASK}_run-{RUN}_space-fsLR_den-91k_desc-residual_timeseries.ptseries.nii \
+      {SUB}_ses-{SESSION}_task-{TASK}_run-{RUN}_space-fsLR_den-91k_desc-residual_boldmap.pconn.nii
 
 More information can be found at the HCP
 `documentation <https://www.humanconnectome.org/software/workbench-command>`_.
diff --git a/xcp_d/cli/combineqc.py b/xcp_d/cli/combineqc.py
index ce43790..2958f31 100644
--- a/xcp_d/cli/combineqc.py
+++ b/xcp_d/cli/combineqc.py
@@ -33,17 +33,17 @@ def main(args=None):
     opts = get_parser().parse_args(args)
 
     xcpd_dir = os.path.abspath(opts.xcpd_dir)
-    outputfile = os.path.join(os.getcwd(), f"{opts.output_prefix}_allsubjects_qc.csv")
+    outputfile = os.path.join(os.getcwd(), f"{opts.output_prefix}_allsubjects_qc.tsv")
 
     qc_files = []
     for dirpath, _, filenames in os.walk(xcpd_dir):
         for filename in filenames:
-            if filename.endswith("_desc-linc_qc.csv"):
+            if filename.endswith("_desc-linc_qc.tsv"):
                 qc_files.append(os.path.join(dirpath, filename))
 
-    dfs = [pd.read_csv(qc_file) for qc_file in qc_files]
+    dfs = [pd.read_table(qc_file) for qc_file in qc_files]
     df = pd.concat(dfs, axis=0)
-    df.to_csv(outputfile, index=False)
+    df.to_csv(outputfile, index=False, sep="\t")
 
 
 if __name__ == "__main__":
diff --git a/xcp_d/data/xcp_d_bids_config.json b/xcp_d/data/xcp_d_bids_config.json
index 159226f..8003953 100755
--- a/xcp_d/data/xcp_d_bids_config.json
+++ b/xcp_d/data/xcp_d_bids_config.json
@@ -11,42 +11,42 @@
       "dtype": "int"
     },
     {
-      "name": "measure",
-      "pattern": "(?:^|_)measure-([a-zA-Z0-9]+)"
+      "name": "statistic",
+      "pattern": "(?:^|_)stat-([a-zA-Z0-9]+)"
+    },
+    {
+      "name": "segmentation",
+      "pattern": "seg-([a-zA-Z0-9]+)"
     }
   ],
   "default_path_patterns": [
     "[desc-{desc}]_{suffix<qc>}{extension<.json>|.json}",
-    "atlases/atlas-{atlas}/[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_res-{res}][_desc-{desc}]_{suffix<dseg>}{extension<.nii|.nii.gz|.tsv|.json>|.nii.gz}",
-    "atlases/atlas-{atlas}/[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<dseg>}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_res-{res}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "atlases/atlas-{atlas}/atlas-{atlas}[_space-{space}][_cohort-{cohort}][_res-{res}][_desc-{desc}]_{suffix<dseg>}{extension<.nii|.nii.gz|.tsv|.json>|.nii.gz}",
+    "atlases/atlas-{atlas}/atlas-{atlas}[_space-{space}][_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<dseg>}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_den-{den}]_hemi-{hemi<L|R>}[_desc-{desc}]_{suffix<wm|smoothwm|white|pial|midthickness|inflated|vinflated|sphere|flat>}{extension<.surf.gii|.json>|.surf.gii}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<sulc|curv|thickness|myelinw>}{extension<.dscalar.nii|.json>|.dscalar.nii}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<morph>}{extension<.tsv|.json>|.tsv}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_res-{res}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_res-{res}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_res-{res}][_desc-{desc}]_{suffix<bold|cbv|phase|sbref|boldref|dseg|alff|reho>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_res-{res}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_measure-{measure}][_desc-{desc}]_{suffix<conmat>|conmat}{extension<.tsv|.json>|.tsv}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<coverage|alff|reho>|coverage}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}]_hemi-{hemi<L|R>}[_desc-{desc}]_{suffix<wm|smoothwm|white|pial|midthickness|inflated|vinflated|sphere|flat>}{extension<.surf.gii|.json>|.surf.gii}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}][_desc-{desc}]_{suffix<sulc|curv|thickness|myelinw>}{extension<.dscalar.nii|.json>|.dscalar.nii}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{res}][_desc-{desc}]_{suffix<bold|sbref|boldref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>}{extension<.txt|.h5>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}]_desc-{desc}_{suffix<mask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}]_stat-{statistic}[_desc-{desc}]_{suffix<relmat>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat|func>|func}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}][_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<bold|morph>}{extension<.tsv|.json>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_desc-{desc}]_{suffix<design>|design}{extension<.tsv|.json>|.tsv}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<AROMAnoiseICs>|AROMAnoiseICs}{extension<.csv|.tsv>|.csv}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<regressors|timeseries>|timeseries}{extension<.json|.tsv|.csv|>|.tsv}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<components|mixing>|components}{extension<.json|.tsv|.csv|.nii|.nii.gz>|.tsv}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<decomposition>|decomposition}{extension<.json|.tsv|.csv>|.json}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_desc-{desc}]_{suffix<motion>}{extension<.json|.tsv>|.tsv}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_desc-{desc}]_{suffix<outliers>}{extension<.json|.tsv>|.tsv}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<qc>}{extension<.json|.csv|.tsv>|.csv}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_res-{res}][_den-{den}]_stat-{statistic}[_desc-{desc}]_{suffix<timeseries>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_desc-{desc}]_{suffix<motion|outliers>}{extension<.json|.tsv>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{res}][_den-{den}][_desc-{desc}]_{suffix<qc>}{extension<.tsv|.json>|.tsv}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_desc-{desc}]_{suffix<qc>}{extension<.hdf5>|.hdf5}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<bold>}{extension<.ptseries.nii|.dtseries.nii|.func.gii|.shape.gii|.json>}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<alff|reho>}{extension<.dscalar.nii|.func.gii|.shape.gii|.json>}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}][_measure-{measure}][_desc-{desc}]_{suffix<timeseries>|timeseries}{extension<.ptseries.nii|.json>}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}][_measure-{measure}][_desc-{desc}]_{suffix<conmat>|conmat}{extension<.pconn.nii|.json>}",
-    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<coverage|alff|reho>|coverage}{extension<.pscalar.nii|.json>}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<bold>}{extension<.dtseries.nii|.json>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.dscalar.nii|.json>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<timeseries>}{extension<.ptseries.nii|.json>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pscalar.nii|.json>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}]_seg-{segmentation}[_den-{den}][_hemi-{hemi<L|R>}]_stat-{statistic}[_desc-{desc}]_{suffix<boldmap>}{extension<.pconn.nii|.json>}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_seg-{segmentation}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<bold|motion>}{extension<.html|.svg|.png>}",
     "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_desc-{desc}]_{suffix<design>|design}{extension<.html|.svg|.png>}"
   ]
diff --git a/xcp_d/interfaces/bids.py b/xcp_d/interfaces/bids.py
index bfdc4bc..168a919 100644
--- a/xcp_d/interfaces/bids.py
+++ b/xcp_d/interfaces/bids.py
@@ -284,9 +284,9 @@ class CopyAtlas(SimpleInterface):
             res_str = f"_res-{res}" if res else ""
             den_str = f"_den-{den}" if den else ""
             if extension == ".dlabel.nii":
-                out_basename = f"space-{space}_atlas-{atlas}{den_str}{cohort_str}_dseg{extension}"
+                out_basename = f"atlas-{atlas}_space-{space}{den_str}{cohort_str}_dseg{extension}"
             elif extension == ".nii.gz":
-                out_basename = f"space-{space}_atlas-{atlas}{res_str}{cohort_str}_dseg{extension}"
+                out_basename = f"atlas-{atlas}_space-{space}{res_str}{cohort_str}_dseg{extension}"
 
         os.makedirs(atlas_out_dir, exist_ok=True)
         out_file = os.path.join(atlas_out_dir, out_basename)
diff --git a/xcp_d/interfaces/plotting.py b/xcp_d/interfaces/plotting.py
index d48bc55..d74aa50 100644
--- a/xcp_d/interfaces/plotting.py
+++ b/xcp_d/interfaces/plotting.py
@@ -525,11 +525,11 @@ class QCPlots(SimpleInterface):
         df = pd.DataFrame(qc_values_dict)
         self._results["qc_file"] = fname_presuffix(
             self.inputs.cleaned_file,
-            suffix="qc_bold.csv",
+            suffix="qc_bold.tsv",
             newpath=runtime.cwd,
             use_ext=False,
         )
-        df.to_csv(self._results["qc_file"], index=False, header=True)
+        df.to_csv(self._results["qc_file"], index=False, header=True, sep="\t")
 
         # Write out the metadata file
         self._results["qc_metadata"] = fname_presuffix(
diff --git a/xcp_d/interfaces/report.py b/xcp_d/interfaces/report.py
index e960cac..5ca4ba0 100644
--- a/xcp_d/interfaces/report.py
+++ b/xcp_d/interfaces/report.py
@@ -145,7 +145,7 @@ class FunctionalSummary(SummaryInterface):
 
     def _generate_segment(self):
         space = get_entity(self.inputs.bold_file, "space")
-        qcfile = pd.read_csv(self.inputs.qc_file)
+        qcfile = pd.read_table(self.inputs.qc_file)
         mean_fd = str(round(qcfile["mean_fd"][0], 4))
         mean_relative_rms = str(round(qcfile["mean_relative_rms"][0], 4))
         max_relative_rms = str(round(qcfile["max_relative_rms"][0], 4))
diff --git a/xcp_d/utils/bids.py b/xcp_d/utils/bids.py
index fb726c0..d00df60 100644
--- a/xcp_d/utils/bids.py
+++ b/xcp_d/utils/bids.py
@@ -676,7 +676,7 @@ def collect_run_data(layout, bold_file, cifti, target_space):
     return run_data
 
 
-def write_dataset_description(fmri_dir, xcpd_dir, custom_confounds_folder=None):
+def write_dataset_description(fmri_dir, xcpd_dir, atlases=None, custom_confounds_folder=None):
     """Write dataset_description.json file for derivatives.
 
     Parameters
@@ -685,6 +685,10 @@ def write_dataset_description(fmri_dir, xcpd_dir, custom_confounds_folder=None):
         Path to the BIDS derivative dataset being ingested.
     xcpd_dir : :obj:`str`
         Path to the output xcp-d dataset.
+    atlases : :obj:`list` of :obj:`str`, optional
+        Names of requested XCP-D atlases.
+    custom_confounds_folder : :obj:`str`, optional
+        Path to the folder containing custom confounds files.
     """
     import json
     import os
@@ -732,6 +736,12 @@ def write_dataset_description(fmri_dir, xcpd_dir, custom_confounds_folder=None):
 
     dset_desc["DatasetLinks"]["preprocessed"] = str(fmri_dir)
 
+    if atlases:
+        if "atlases" in dset_desc["DatasetLinks"].keys():
+            LOGGER.warning("'atlases' is already a dataset link. Overwriting.")
+
+        dset_desc["DatasetLinks"]["atlases"] = os.path.join(xcpd_dir, "atlases")
+
     if custom_confounds_folder:
         if "custom_confounds" in dset_desc["DatasetLinks"].keys():
             LOGGER.warning("'custom_confounds' is already a dataset link. Overwriting.")
@@ -752,6 +762,47 @@ def write_dataset_description(fmri_dir, xcpd_dir, custom_confounds_folder=None):
             json.dump(dset_desc, fo, indent=4, sort_keys=True)
 
 
+def write_atlas_dataset_description(atlas_dir):
+    """Write dataset_description.json file for Atlas derivatives.
+
+    Parameters
+    ----------
+    atlas_dir : :obj:`str`
+        Path to the output XCP-D Atlases dataset.
+    """
+    import json
+    import os
+
+    from xcp_d.__about__ import DOWNLOAD_URL, __version__
+
+    dset_desc = {
+        "Name": "XCP-D Atlases",
+        "DatasetType": "atlas",
+        "GeneratedBy": [
+            {
+                "Name": "xcp_d",
+                "Version": __version__,
+                "CodeURL": DOWNLOAD_URL,
+            },
+        ],
+        "HowToAcknowledge": "Include the generated boilerplate in the methods section.",
+    }
+    os.makedirs(atlas_dir, exist_ok=True)
+
+    atlas_dset_description = os.path.join(atlas_dir, "dataset_description.json")
+    if os.path.isfile(atlas_dset_description):
+        with open(atlas_dset_description, "r") as fo:
+            old_dset_desc = json.load(fo)
+
+        old_version = old_dset_desc["GeneratedBy"][0]["Version"]
+        if Version(__version__).public != Version(old_version).public:
+            LOGGER.warning(f"Previous output generated by version {old_version} found.")
+
+    else:
+        with open(atlas_dset_description, "w") as fo:
+            json.dump(dset_desc, fo, indent=4, sort_keys=True)
+
+
 def get_preproc_pipeline_info(input_type, fmri_dir):
     """Get preprocessing pipeline information from the dataset_description.json file."""
     import json
@@ -1018,6 +1069,20 @@ def _make_xcpd_uri_lol(in_list, output_dir):
     return out_lol
 
 
+def _make_atlas_uri(out_file, output_dir):
+    """Convert postprocessing atlas derivative's path to BIDS URI."""
+    import os
+
+    from xcp_d.utils.bids import _make_uri
+
+    dataset_path = os.path.join(output_dir, "xcp_d", "atlases")
+
+    if isinstance(out_file, list):
+        return [_make_uri(of, "atlas", dataset_path) for of in out_file]
+    else:
+        return [_make_uri(out_file, "atlas", dataset_path)]
+
+
 def _make_preproc_uri(out_file, fmri_dir):
     """Convert preprocessing derivative's path to BIDS URI."""
     from xcp_d.utils.bids import _make_uri
diff --git a/xcp_d/workflows/base.py b/xcp_d/workflows/base.py
index 91f59f4..c6a5594 100644
--- a/xcp_d/workflows/base.py
+++ b/xcp_d/workflows/base.py
@@ -30,6 +30,7 @@ from xcp_d.utils.bids import (
     get_entity,
     get_preproc_pipeline_info,
     group_across_runs,
+    write_atlas_dataset_description,
     write_dataset_description,
 )
 from xcp_d.utils.doc import fill_doc
@@ -196,7 +197,14 @@ def init_xcpd_wf(
     xcpd_wf.base_dir = work_dir
     LOGGER.info(f"Beginning the {name} workflow")
 
-    write_dataset_description(fmri_dir, os.path.join(output_dir, "xcp_d"))
+    write_dataset_description(
+        fmri_dir,
+        os.path.join(output_dir, "xcp_d"),
+        atlases=atlases,
+        custom_confounds_folder=custom_confounds_folder,
+    )
+    if atlases:
+        write_atlas_dataset_description(os.path.join(output_dir, "xcp_d", "atlases"))
 
     for subject_id in subject_list:
         single_subj_wf = init_subject_wf(
diff --git a/xcp_d/workflows/concatenation.py b/xcp_d/workflows/concatenation.py
index f5d7be5..b4d325b 100644
--- a/xcp_d/workflows/concatenation.py
+++ b/xcp_d/workflows/concatenation.py
@@ -214,7 +214,7 @@ Postprocessing derivatives from multi-run tasks were then concatenated across ru
     ds_filtered_motion = pe.Node(
         DerivativesDataSink(
             base_directory=output_dir,
-            dismiss_entities=["atlas", "den", "res", "space", "cohort", "desc"],
+            dismiss_entities=["segmentation", "den", "res", "space", "cohort", "desc"],
             desc="filtered" if motion_filter_type else None,
             suffix="motion",
             extension=".tsv",
@@ -234,7 +234,7 @@ Postprocessing derivatives from multi-run tasks were then concatenated across ru
     ds_temporal_mask = pe.Node(
         DerivativesDataSink(
             base_directory=output_dir,
-            dismiss_entities=["atlas", "den", "res", "space", "cohort", "desc"],
+            dismiss_entities=["segmentation", "den", "res", "space", "cohort", "desc"],
             suffix="outliers",
             extension=".tsv",
         ),
@@ -384,7 +384,8 @@ Postprocessing derivatives from multi-run tasks were then concatenated across ru
         ds_timeseries = pe.MapNode(
             DerivativesDataSink(
                 base_directory=output_dir,
-                dismiss_entities=["desc"],
+                dismiss_entities=["desc", "den", "res"],
+                statistic="mean",
                 suffix="timeseries",
                 extension=".tsv",
                 # Metadata
@@ -393,9 +394,9 @@ Postprocessing derivatives from multi-run tasks were then concatenated across ru
             name="ds_timeseries",
             run_without_submitting=True,
             mem_gb=1,
-            iterfield=["atlas", "in_file", "meta_dict"],
+            iterfield=["segmentation", "in_file", "meta_dict"],
         )
-        ds_timeseries.inputs.atlas = atlases
+        ds_timeseries.inputs.segmentation = atlases
 
         workflow.connect([
             (clean_name_source, ds_timeseries, [("name_source", "source_file")]),
@@ -435,16 +436,16 @@ Postprocessing derivatives from multi-run tasks were then concatenated across ru
             DerivativesDataSink(
                 base_directory=output_dir,
                 dismiss_entities=["desc"],
-                measure="pearsoncorrelation",
-                suffix="conmat",
+                statistic="pearsoncorrelation",
+                suffix="relmat",
                 extension=".tsv",
             ),
             name="ds_correlations",
             run_without_submitting=True,
             mem_gb=1,
-            iterfield=["atlas", "in_file", "meta_dict"],
+            iterfield=["segmentation", "in_file", "meta_dict"],
         )
-        ds_correlations.inputs.atlas = atlases
+        ds_correlations.inputs.segmentation = atlases
 
         workflow.connect([
             (clean_name_source, ds_correlations, [("name_source", "source_file")]),
@@ -476,15 +477,16 @@ Postprocessing derivatives from multi-run tasks were then concatenated across ru
                     check_hdr=False,
                     dismiss_entities=["desc", "den"],
                     den="91k",
+                    statistic="mean",
                     suffix="timeseries",
                     extension=".ptseries.nii",
                 ),
                 name="ds_timeseries_cifti_files",
                 run_without_submitting=True,
                 mem_gb=1,
-                iterfield=["atlas", "in_file", "meta_dict"],
+                iterfield=["segmentation", "in_file", "meta_dict"],
             )
-            ds_timeseries_cifti_files.inputs.atlas = atlases
+            ds_timeseries_cifti_files.inputs.segmentation = atlases
 
             workflow.connect([
                 (clean_name_source, ds_timeseries_cifti_files, [("name_source", "source_file")]),
diff --git a/xcp_d/workflows/connectivity.py b/xcp_d/workflows/connectivity.py
index 643651a..4aa7956 100644
--- a/xcp_d/workflows/connectivity.py
+++ b/xcp_d/workflows/connectivity.py
@@ -406,17 +406,18 @@ def init_parcellate_surfaces_wf(
         ds_parcellated_surface = pe.MapNode(
             DerivativesDataSink(
                 base_directory=output_dir,
-                dismiss_entities=["hemi", "desc"],
+                dismiss_entities=["hemi", "desc", "den", "res"],
                 desc=SURF_DESCS[file_to_parcellate],
+                statistic="mean",
                 suffix="morph",
                 extension=".tsv",
             ),
             name=f"ds_parcellated_{file_to_parcellate}",
             run_without_submitting=True,
             mem_gb=1,
-            iterfield=["atlas", "in_file"],
+            iterfield=["segmentation", "in_file"],
         )
-        ds_parcellated_surface.inputs.atlas = selected_atlases
+        ds_parcellated_surface.inputs.segmentation = selected_atlases
 
         # fmt:off
         workflow.connect([
diff --git a/xcp_d/workflows/outputs.py b/xcp_d/workflows/outputs.py
index b8d448d..4813670 100644
--- a/xcp_d/workflows/outputs.py
+++ b/xcp_d/workflows/outputs.py
@@ -8,6 +8,7 @@ from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from xcp_d.interfaces.bids import DerivativesDataSink
 from xcp_d.interfaces.utils import FilterUndefined
 from xcp_d.utils.bids import (
+    _make_atlas_uri,
     _make_custom_uri,
     _make_preproc_uri,
     _make_xcpd_uri,
@@ -289,7 +290,7 @@ def init_postproc_derivatives_wf(
 
     # Create dictionary of basic information
     cleaned_data_dictionary = {
-        "nuisance parameters": params,
+        "NuisanceParameters": params,
         **source_metadata,
     }
     software_filters = None
@@ -321,7 +322,7 @@ def init_postproc_derivatives_wf(
         DerivativesDataSink(
             base_directory=output_dir,
             source_file=name_source,
-            dismiss_entities=["atlas", "den", "res", "space", "cohort", "desc"],
+            dismiss_entities=["segmentation", "den", "res", "space", "cohort", "desc"],
             desc="filtered" if motion_filter_type else None,
             suffix="motion",
             extension=".tsv",
@@ -353,7 +354,7 @@ def init_postproc_derivatives_wf(
         ds_temporal_mask = pe.Node(
             DerivativesDataSink(
                 base_directory=output_dir,
-                dismiss_entities=["atlas", "den", "res", "space", "cohort", "desc"],
+                dismiss_entities=["segmentation", "den", "res", "space", "cohort", "desc"],
                 suffix="outliers",
                 extension=".tsv",
                 source_file=name_source,
@@ -499,12 +500,12 @@ def init_postproc_derivatives_wf(
         DerivativesDataSink(
             base_directory=output_dir,
             source_file=name_source,
-            dismiss_entities=["desc", "den"],
+            dismiss_entities=["desc", "den", "res"],
             cohort=cohort,
             den="91k" if cifti else None,
             desc="linc",
             suffix="qc",
-            extension=".csv",
+            extension=".tsv",
         ),
         name="ds_qc_file",
         run_without_submitting=True,
@@ -557,7 +558,7 @@ def init_postproc_derivatives_wf(
         )
         workflow.connect([
             (inputnode, make_atlas_dict, [
-                (("atlas_files", _make_xcpd_uri, output_dir), "Sources"),
+                (("atlas_files", _make_atlas_uri, output_dir), "Sources"),
             ]),
         ])  # fmt:skip
 
@@ -587,17 +588,18 @@ def init_postproc_derivatives_wf(
             DerivativesDataSink(
                 base_directory=output_dir,
                 source_file=name_source,
-                dismiss_entities=["desc"],
+                dismiss_entities=["desc", "den", "res"],
                 cohort=cohort,
-                suffix="coverage",
+                statistic="coverage",
+                suffix="bold",
                 extension=".tsv",
             ),
             name="ds_coverage",
             run_without_submitting=True,
             mem_gb=1,
-            iterfield=["atlas", "in_file", "meta_dict"],
+            iterfield=["segmentation", "in_file", "meta_dict"],
         )
-        ds_coverage.inputs.atlas = atlases
+        ds_coverage.inputs.segmentation = atlases
         # fmt:off
         workflow.connect([
             (inputnode, ds_coverage, [("coverage", "in_file")]),
@@ -629,8 +631,9 @@ def init_postproc_derivatives_wf(
             DerivativesDataSink(
                 base_directory=output_dir,
                 source_file=name_source,
-                dismiss_entities=["desc"],
+                dismiss_entities=["desc", "den", "res"],
                 cohort=cohort,
+                statistic="mean",
                 suffix="timeseries",
                 extension=".tsv",
                 # Metadata
@@ -639,9 +642,9 @@ def init_postproc_derivatives_wf(
             name="ds_timeseries",
             run_without_submitting=True,
             mem_gb=1,
-            iterfield=["atlas", "in_file", "meta_dict"],
+            iterfield=["segmentation", "in_file", "meta_dict"],
         )
-        ds_timeseries.inputs.atlas = atlases
+        ds_timeseries.inputs.segmentation = atlases
         # fmt:off
         workflow.connect([
             (inputnode, ds_timeseries, [("timeseries", "in_file")]),
@@ -653,32 +656,45 @@ def init_postproc_derivatives_wf(
         make_corrs_meta_dict = pe.MapNode(
             niu.Function(
                 function=_make_dictionary,
-                input_names=["Sources"],
+                input_names=["Sources", "NodeFiles"],
                 output_names=["metadata"],
             ),
             run_without_submitting=True,
             mem_gb=1,
             name="make_corrs_meta_dict",
-            iterfield=["Sources"],
+            iterfield=["Sources", "NodeFiles"],
         )
-        workflow.connect([(ds_timeseries, make_corrs_meta_dict, [("out_file", "Sources")])])
+        workflow.connect([
+            (inputnode, make_corrs_meta_dict, [
+                (("atlas_files", _make_atlas_uri, output_dir), "NodeFiles"),
+            ]),
+            (ds_timeseries, make_corrs_meta_dict, [
+                (("out_file", _make_xcpd_uri, output_dir), "Sources"),
+            ]),
+        ])  # fmt:skip
 
         ds_correlations = pe.MapNode(
             DerivativesDataSink(
                 base_directory=output_dir,
                 source_file=name_source,
-                dismiss_entities=["desc"],
+                dismiss_entities=["desc", "den", "res"],
                 cohort=cohort,
-                measure="pearsoncorrelation",
-                suffix="conmat",
+                statistic="pearsoncorrelation",
+                suffix="relmat",
                 extension=".tsv",
+                # Metadata
+                RelationshipMeasure="Pearson correlation coefficient",
+                Weighted=True,
+                Directed=False,
+                ValidDiagonal=False,
+                StorageFormat="Full",
             ),
             name="ds_correlations",
             run_without_submitting=True,
             mem_gb=1,
-            iterfield=["atlas", "in_file", "meta_dict"],
+            iterfield=["segmentation", "in_file", "meta_dict"],
         )
-        ds_correlations.inputs.atlas = atlases
+        ds_correlations.inputs.segmentation = atlases
         # fmt:off
         workflow.connect([
             (inputnode, ds_correlations, [("correlations", "in_file")]),
@@ -694,15 +710,16 @@ def init_postproc_derivatives_wf(
                     check_hdr=False,
                     dismiss_entities=["desc"],
                     cohort=cohort,
-                    suffix="coverage",
+                    statistic="coverage",
+                    suffix="boldmap",
                     extension=".pscalar.nii",
                 ),
                 name="ds_coverage_ciftis",
                 run_without_submitting=True,
                 mem_gb=1,
-                iterfield=["atlas", "in_file", "meta_dict"],
+                iterfield=["segmentation", "in_file", "meta_dict"],
             )
-            ds_coverage_ciftis.inputs.atlas = atlases
+            ds_coverage_ciftis.inputs.segmentation = atlases
             # fmt:off
             workflow.connect([
                 (inputnode, ds_coverage_ciftis, [("coverage_ciftis", "in_file")]),
@@ -738,15 +755,16 @@ def init_postproc_derivatives_wf(
                     dismiss_entities=["desc", "den"],
                     cohort=cohort,
                     den="91k" if cifti else None,
+                    statistic="mean",
                     suffix="timeseries",
                     extension=".ptseries.nii",
                 ),
                 name="ds_timeseries_ciftis",
                 run_without_submitting=True,
                 mem_gb=1,
-                iterfield=["atlas", "in_file", "meta_dict"],
+                iterfield=["segmentation", "in_file", "meta_dict"],
             )
-            ds_timeseries_ciftis.inputs.atlas = atlases
+            ds_timeseries_ciftis.inputs.segmentation = atlases
             # fmt:off
             workflow.connect([
                 (inputnode, ds_timeseries_ciftis, [("timeseries_ciftis", "in_file")]),
@@ -758,19 +776,22 @@ def init_postproc_derivatives_wf(
             make_ccorrs_meta_dict = pe.MapNode(
                 niu.Function(
                     function=_make_dictionary,
-                    input_names=["Sources"],
+                    input_names=["Sources", "NodeFiles"],
                     output_names=["metadata"],
                 ),
                 run_without_submitting=True,
                 mem_gb=1,
                 name="make_ccorrs_meta_dict",
-                iterfield=["Sources"],
+                iterfield=["Sources", "NodeFiles"],
             )
-            # fmt:off
             workflow.connect([
-                (ds_timeseries_ciftis, make_ccorrs_meta_dict, [("out_file", "Sources")]),
-            ])
-            # fmt:on
+                (inputnode, make_ccorrs_meta_dict, [
+                    (("atlas_files", _make_atlas_uri, output_dir), "NodeFiles"),
+                ]),
+                (ds_timeseries_ciftis, make_ccorrs_meta_dict, [
+                    (("out_file", _make_xcpd_uri, output_dir), "Sources"),
+                ]),
+            ])  # fmt:skip
 
             ds_correlation_ciftis = pe.MapNode(
                 DerivativesDataSink(
@@ -780,19 +801,27 @@ def init_postproc_derivatives_wf(
                     dismiss_entities=["desc", "den"],
                     cohort=cohort,
                     den="91k" if cifti else None,
-                    measure="pearsoncorrelation",
-                    suffix="conmat",
+                    statistic="pearsoncorrelation",
+                    suffix="boldmap",
                     extension=".pconn.nii",
+                    # Metadata
+                    RelationshipMeasure="Pearson correlation coefficient",
+                    Weighted=True,
+                    Directed=False,
+                    ValidDiagonal=False,
+                    StorageFormat="Full",
                 ),
                 name="ds_correlation_ciftis",
                 run_without_submitting=True,
                 mem_gb=1,
-                iterfield=["atlas", "in_file", "meta_dict"],
+                iterfield=["segmentation", "in_file", "meta_dict"],
             )
-            ds_correlation_ciftis.inputs.atlas = atlases
+            ds_correlation_ciftis.inputs.segmentation = atlases
             # fmt:off
             workflow.connect([
-                (inputnode, ds_correlation_ciftis, [("correlation_ciftis", "in_file")]),
+                (inputnode, ds_correlation_ciftis, [
+                    ("correlation_ciftis", "in_file"),
+                ]),
                 (make_ccorrs_meta_dict, ds_correlation_ciftis, [("metadata", "meta_dict")]),
             ])
             # fmt:on
@@ -813,19 +842,19 @@ def init_postproc_derivatives_wf(
                 DerivativesDataSink(
                     base_directory=output_dir,
                     source_file=name_source,
-                    dismiss_entities=["desc"],
+                    dismiss_entities=["desc", "den", "res"],
                     cohort=cohort,
-                    measure="pearsoncorrelation",
+                    statistic="pearsoncorrelation",
                     desc=f"{exact_scan}volumes",
-                    suffix="conmat",
+                    suffix="relmat",
                     extension=".tsv",
                 ),
                 name=f"ds_correlations_exact_{i_exact_scan}",
                 run_without_submitting=True,
                 mem_gb=1,
-                iterfield=["atlas", "in_file"],
+                iterfield=["segmentation", "in_file"],
             )
-            ds_correlations_exact.inputs.atlas = atlases
+            ds_correlations_exact.inputs.segmentation = atlases
             # fmt:off
             workflow.connect([
                 (select_exact_scan_files, ds_correlations_exact, [("out", "in_file")]),
@@ -841,7 +870,8 @@ def init_postproc_derivatives_wf(
             dismiss_entities=["desc", "den"],
             cohort=cohort,
             den="91k" if cifti else None,
-            suffix="reho",
+            statistic="reho",
+            suffix="boldmap",
             extension=".dscalar.nii" if cifti else ".nii.gz",
             # Metadata
             SoftwareFilters=software_filters,
@@ -881,9 +911,10 @@ def init_postproc_derivatives_wf(
             DerivativesDataSink(
                 base_directory=output_dir,
                 source_file=name_source,
-                dismiss_entities=["desc"],
+                dismiss_entities=["desc", "den", "res"],
                 cohort=cohort,
-                suffix="reho",
+                statistic="reho",
+                suffix="bold",
                 extension=".tsv",
                 # Metadata
                 SoftwareFilters=software_filters,
@@ -892,9 +923,9 @@ def init_postproc_derivatives_wf(
             name="ds_parcellated_reho",
             run_without_submitting=True,
             mem_gb=1,
-            iterfield=["atlas", "in_file", "meta_dict"],
+            iterfield=["segmentation", "in_file", "meta_dict"],
         )
-        ds_parcellated_reho.inputs.atlas = atlases
+        ds_parcellated_reho.inputs.segmentation = atlases
         # fmt:off
         workflow.connect([
             (inputnode, ds_parcellated_reho, [("parcellated_reho", "in_file")]),
@@ -911,7 +942,8 @@ def init_postproc_derivatives_wf(
                 dismiss_entities=["desc", "den"],
                 cohort=cohort,
                 den="91k" if cifti else None,
-                suffix="alff",
+                statistic="alff",
+                suffix="boldmap",
                 extension=".dscalar.nii" if cifti else ".nii.gz",
                 # Metadata
                 SoftwareFilters=software_filters,
@@ -923,9 +955,7 @@ def init_postproc_derivatives_wf(
         # fmt:off
         workflow.connect([
             (inputnode, ds_alff, [("alff", "in_file")]),
-            (ds_denoised_bold, ds_alff, [
-                (("out_file", _make_xcpd_uri, output_dir), "Sources"),
-            ]),
+            (ds_denoised_bold, ds_alff, [(("out_file", _make_xcpd_uri, output_dir), "Sources")]),
         ])
         # fmt:on
 
@@ -938,7 +968,8 @@ def init_postproc_derivatives_wf(
                     cohort=cohort,
                     desc="smooth",
                     den="91k" if cifti else None,
-                    suffix="alff",
+                    statistic="alff",
+                    suffix="boldmap",
                     extension=".dscalar.nii" if cifti else ".nii.gz",
                     check_hdr=False,
                     # Metadata
@@ -983,17 +1014,18 @@ def init_postproc_derivatives_wf(
                 DerivativesDataSink(
                     base_directory=output_dir,
                     source_file=name_source,
-                    dismiss_entities=["desc"],
+                    dismiss_entities=["desc", "den", "res"],
                     cohort=cohort,
-                    suffix="alff",
+                    statistic="alff",
+                    suffix="bold",
                     extension=".tsv",
                 ),
                 name="ds_parcellated_alff",
                 run_without_submitting=True,
                 mem_gb=1,
-                iterfield=["atlas", "in_file", "meta_dict"],
+                iterfield=["segmentation", "in_file", "meta_dict"],
             )
-            ds_parcellated_alff.inputs.atlas = atlases
+            ds_parcellated_alff.inputs.segmentation = atlases
             # fmt:off
             workflow.connect([
                 (inputnode, ds_parcellated_alff, [("parcellated_alff", "in_file")]),


Test patch:
diff --git a/xcp_d/tests/data/test_ds001419_cifti_outputs.txt b/xcp_d/tests/data/test_ds001419_cifti_outputs.txt
index af20bb0..38f5482 100644
--- a/xcp_d/tests/data/test_ds001419_cifti_outputs.txt
+++ b/xcp_d/tests/data/test_ds001419_cifti_outputs.txt
@@ -1,60 +1,61 @@
 xcp_d/atlases
+xcp_d/atlases/dataset_description.json
 xcp_d/atlases/atlas-4S1056Parcels
 xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.json
 xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S1056Parcels/space-fsLR_atlas-4S1056Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-4S156Parcels
 xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.json
 xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S156Parcels/space-fsLR_atlas-4S156Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-4S256Parcels
 xcp_d/atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.json
 xcp_d/atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S256Parcels/space-fsLR_atlas-4S256Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S256Parcels/atlas-4S256Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-4S356Parcels
 xcp_d/atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.json
 xcp_d/atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S356Parcels/space-fsLR_atlas-4S356Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S356Parcels/atlas-4S356Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-4S456Parcels
 xcp_d/atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.json
 xcp_d/atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S456Parcels/space-fsLR_atlas-4S456Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S456Parcels/atlas-4S456Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-4S556Parcels
 xcp_d/atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.json
 xcp_d/atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S556Parcels/space-fsLR_atlas-4S556Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S556Parcels/atlas-4S556Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-4S656Parcels
 xcp_d/atlases/atlas-4S656Parcels/atlas-4S656Parcels_dseg.json
 xcp_d/atlases/atlas-4S656Parcels/atlas-4S656Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S656Parcels/space-fsLR_atlas-4S656Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S656Parcels/atlas-4S656Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-4S756Parcels
 xcp_d/atlases/atlas-4S756Parcels/atlas-4S756Parcels_dseg.json
 xcp_d/atlases/atlas-4S756Parcels/atlas-4S756Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S756Parcels/space-fsLR_atlas-4S756Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S756Parcels/atlas-4S756Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-4S856Parcels
 xcp_d/atlases/atlas-4S856Parcels/atlas-4S856Parcels_dseg.json
 xcp_d/atlases/atlas-4S856Parcels/atlas-4S856Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S856Parcels/space-fsLR_atlas-4S856Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S856Parcels/atlas-4S856Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-4S956Parcels
 xcp_d/atlases/atlas-4S956Parcels/atlas-4S956Parcels_dseg.json
 xcp_d/atlases/atlas-4S956Parcels/atlas-4S956Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S956Parcels/space-fsLR_atlas-4S956Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S956Parcels/atlas-4S956Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-Glasser
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.json
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.tsv
-xcp_d/atlases/atlas-Glasser/space-fsLR_atlas-Glasser_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-Glasser/atlas-Glasser_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-Gordon
 xcp_d/atlases/atlas-Gordon/atlas-Gordon_dseg.json
 xcp_d/atlases/atlas-Gordon/atlas-Gordon_dseg.tsv
-xcp_d/atlases/atlas-Gordon/space-fsLR_atlas-Gordon_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-Gordon/atlas-Gordon_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-HCP
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.json
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.tsv
-xcp_d/atlases/atlas-HCP/space-fsLR_atlas-HCP_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-HCP/atlas-HCP_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-Tian
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.json
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.tsv
-xcp_d/atlases/atlas-Tian/space-fsLR_atlas-Tian_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-Tian/atlas-Tian_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/dataset_description.json
 xcp_d/desc-linc_qc.json
 xcp_d/logs
@@ -77,257 +78,257 @@ xcp_d/sub-01/func/sub-01_task-imagery_run-01_design.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_design.tsv
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_outliers.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_outliers.tsv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_alff.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_alff.tsv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_coverage.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_coverage.tsv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_den-91k_coverage.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_den-91k_coverage.pscalar.nii
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_den-91k_measure-pearsoncorrelation_conmat.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_den-91k_measure-pearsoncorrelation_conmat.pconn.nii
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_den-91k_timeseries.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_den-91k_timeseries.ptseries.nii
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_measure-pearsoncorrelation_conmat.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_measure-pearsoncorrelation_conmat.tsv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_measure-pearsoncorrelation_desc-26volumes_conmat.tsv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_reho.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_reho.tsv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_timeseries.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S1056Parcels_timeseries.tsv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S156Parcels_alff.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S156Parcels_alff.tsv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S156Parcels_coverage.json
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-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S156Parcels_den-91k_measure-pearsoncorrelation_conmat.pconn.nii
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S156Parcels_den-91k_timeseries.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-fsLR_atlas-4S156Parcels_den-91k_timeseries.ptseries.nii
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 xcp_d/sub-01/func/sub-01_task-imagery_run-02_desc-filtered_motion.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_desc-filtered_motion.tsv
@@ -335,341 +336,341 @@ xcp_d/sub-01/func/sub-01_task-imagery_run-02_design.json
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+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-4S556Parcels_stat-pearsoncorrelation_relmat.tsv
+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-4S556Parcels_stat-mean_timeseries.json
+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-4S556Parcels_stat-mean_timeseries.tsv
+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-4S656Parcels_den-91k_stat-mean_timeseries.json
+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-4S656Parcels_den-91k_stat-mean_timeseries.ptseries.nii
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+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-Gordon_den-91k_stat-mean_timeseries.json
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+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-Gordon_stat-mean_timeseries.json
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+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-HCP_den-91k_stat-mean_timeseries.json
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+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-HCP_stat-pearsoncorrelation_relmat.json
+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-HCP_stat-pearsoncorrelation_relmat.tsv
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+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-HCP_stat-mean_timeseries.tsv
+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-Tian_den-91k_stat-mean_timeseries.json
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+xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_seg-Tian_stat-mean_timeseries.json
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 xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_den-91k_desc-denoisedSmoothed_bold.dtseries.nii
 xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_den-91k_desc-denoisedSmoothed_bold.json
 xcp_d/sub-01/func/sub-01_task-imagery_space-fsLR_den-91k_desc-denoised_bold.dtseries.nii
diff --git a/xcp_d/tests/data/test_ds001419_nifti_outputs.txt b/xcp_d/tests/data/test_ds001419_nifti_outputs.txt
index 9a5fdf3..cbdee89 100644
--- a/xcp_d/tests/data/test_ds001419_nifti_outputs.txt
+++ b/xcp_d/tests/data/test_ds001419_nifti_outputs.txt
@@ -18,34 +18,34 @@ xcp_d/sub-01/func/sub-01_task-imagery_run-01_desc-preproc_design.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_desc-preproc_design.tsv
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_outliers.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_outliers.tsv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-MNI152NLin2009cAsym_desc-linc_qc.csv
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-MNI152NLin2009cAsym_res-2_alff.json
-xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-MNI152NLin2009cAsym_res-2_alff.nii.gz
+xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-MNI152NLin2009cAsym_desc-linc_qc.tsv
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 xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-MNI152NLin2009cAsym_res-2_desc-denoisedSmoothed_bold.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-MNI152NLin2009cAsym_res-2_desc-denoisedSmoothed_bold.nii.gz
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-MNI152NLin2009cAsym_res-2_desc-denoised_bold.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-01_space-MNI152NLin2009cAsym_res-2_desc-denoised_bold.nii.gz
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 xcp_d/sub-01/func/sub-01_task-imagery_run-02_desc-filtered_motion.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_desc-filtered_motion.tsv
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_desc-preproc_design.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_desc-preproc_design.tsv
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_outliers.json
 xcp_d/sub-01/func/sub-01_task-imagery_run-02_outliers.tsv
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 xcp_d/sub-01/func/sub-01_task-imagery_run-02_space-MNI152NLin2009cAsym_res-2_desc-denoisedSmoothed_bold.json
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 xcp_d/sub-01/func/sub-01_task-imagery_space-MNI152NLin2009cAsym_res-2_desc-denoisedSmoothed_bold.json
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 xcp_d/sub-01/func/sub-01_task-imagery_space-MNI152NLin2009cAsym_res-2_desc-denoised_bold.json
@@ -56,15 +56,15 @@ xcp_d/sub-01/func/sub-01_task-rest_desc-preproc_design.json
 xcp_d/sub-01/func/sub-01_task-rest_desc-preproc_design.tsv
 xcp_d/sub-01/func/sub-01_task-rest_outliers.json
 xcp_d/sub-01/func/sub-01_task-rest_outliers.tsv
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diff --git a/xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt b/xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt
index 94df7f1..3e87c86 100644
--- a/xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt
+++ b/xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt
@@ -1,60 +1,61 @@
 xcp_d/atlases
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 xcp_d/atlases/atlas-4S1056Parcels
 xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.json
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 xcp_d/atlases/atlas-4S156Parcels
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 xcp_d/atlases/atlas-4S356Parcels
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 xcp_d/atlases/atlas-4S456Parcels
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 xcp_d/atlases/atlas-4S556Parcels
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 xcp_d/atlases/atlas-4S756Parcels
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 xcp_d/atlases/atlas-4S856Parcels
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 xcp_d/atlases/atlas-4S956Parcels
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 xcp_d/atlases/atlas-Glasser
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.json
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.tsv
-xcp_d/atlases/atlas-Glasser/space-MNI152NLin2009cAsym_atlas-Glasser_dseg.nii.gz
+xcp_d/atlases/atlas-Glasser/atlas-Glasser_space-MNI152NLin2009cAsym_dseg.nii.gz
 xcp_d/atlases/atlas-Gordon
 xcp_d/atlases/atlas-Gordon/atlas-Gordon_dseg.json
 xcp_d/atlases/atlas-Gordon/atlas-Gordon_dseg.tsv
-xcp_d/atlases/atlas-Gordon/space-MNI152NLin2009cAsym_atlas-Gordon_dseg.nii.gz
+xcp_d/atlases/atlas-Gordon/atlas-Gordon_space-MNI152NLin2009cAsym_dseg.nii.gz
 xcp_d/atlases/atlas-HCP
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.json
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.tsv
-xcp_d/atlases/atlas-HCP/space-MNI152NLin2009cAsym_atlas-HCP_dseg.nii.gz
+xcp_d/atlases/atlas-HCP/atlas-HCP_space-MNI152NLin2009cAsym_dseg.nii.gz
 xcp_d/atlases/atlas-Tian
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.json
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.tsv
-xcp_d/atlases/atlas-Tian/space-MNI152NLin2009cAsym_atlas-Tian_dseg.nii.gz
+xcp_d/atlases/atlas-Tian/atlas-Tian_space-MNI152NLin2009cAsym_dseg.nii.gz
 xcp_d/dataset_description.json
 xcp_d/desc-linc_qc.json
 xcp_d/logs
@@ -75,127 +76,127 @@ xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_motion.json
 xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_motion.tsv
 xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_outliers.json
 xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_outliers.tsv
-xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S1056Parcels_coverage.json
-xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S1056Parcels_coverage.tsv
-xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S1056Parcels_measure-pearsoncorrelation_conmat.json
-xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S1056Parcels_measure-pearsoncorrelation_conmat.tsv
-xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S1056Parcels_reho.json
-xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S1056Parcels_reho.tsv
-xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-1_space-MNI152NLin2009cAsym_atlas-4S1056Parcels_timeseries.json
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 xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_desc-denoisedSmoothed_bold.json
 xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_desc-denoisedSmoothed_bold.nii.gz
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 xcp_d/sub-01/func/sub-01_task-mixedgamblestask_run-2_space-MNI152NLin2009cAsym_desc-interpolated_bold.json
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 xcp_d/sub-01_executive_summary.html
diff --git a/xcp_d/tests/data/test_nibabies_outputs.txt b/xcp_d/tests/data/test_nibabies_outputs.txt
index 9506dc8..a73908d 100644
--- a/xcp_d/tests/data/test_nibabies_outputs.txt
+++ b/xcp_d/tests/data/test_nibabies_outputs.txt
@@ -1,60 +1,61 @@
 xcp_d/atlases
+xcp_d/atlases/dataset_description.json
 xcp_d/atlases/atlas-4S1056Parcels
 xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.json
 xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S1056Parcels/space-MNIInfant_atlas-4S1056Parcels_cohort-1_dseg.nii.gz
+xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_space-MNIInfant_cohort-1_dseg.nii.gz
 xcp_d/atlases/atlas-4S156Parcels
 xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.json
 xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S156Parcels/space-MNIInfant_atlas-4S156Parcels_cohort-1_dseg.nii.gz
+xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_space-MNIInfant_cohort-1_dseg.nii.gz
 xcp_d/atlases/atlas-4S256Parcels
 xcp_d/atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.json
 xcp_d/atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S256Parcels/space-MNIInfant_atlas-4S256Parcels_cohort-1_dseg.nii.gz
+xcp_d/atlases/atlas-4S256Parcels/atlas-4S256Parcels_space-MNIInfant_cohort-1_dseg.nii.gz
 xcp_d/atlases/atlas-4S356Parcels
 xcp_d/atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.json
 xcp_d/atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S356Parcels/space-MNIInfant_atlas-4S356Parcels_cohort-1_dseg.nii.gz
+xcp_d/atlases/atlas-4S356Parcels/atlas-4S356Parcels_space-MNIInfant_cohort-1_dseg.nii.gz
 xcp_d/atlases/atlas-4S456Parcels
 xcp_d/atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.json
 xcp_d/atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.tsv
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 xcp_d/atlases/atlas-4S556Parcels
 xcp_d/atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.json
 xcp_d/atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.tsv
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 xcp_d/atlases/atlas-4S656Parcels
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 xcp_d/atlases/atlas-4S656Parcels/atlas-4S656Parcels_dseg.tsv
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 xcp_d/atlases/atlas-4S756Parcels
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 xcp_d/atlases/atlas-4S756Parcels/atlas-4S756Parcels_dseg.tsv
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 xcp_d/atlases/atlas-4S856Parcels
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 xcp_d/atlases/atlas-4S956Parcels
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 xcp_d/atlases/atlas-4S956Parcels/atlas-4S956Parcels_dseg.tsv
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 xcp_d/atlases/atlas-Glasser
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.json
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.tsv
-xcp_d/atlases/atlas-Glasser/space-MNIInfant_atlas-Glasser_cohort-1_dseg.nii.gz
+xcp_d/atlases/atlas-Glasser/atlas-Glasser_space-MNIInfant_cohort-1_dseg.nii.gz
 xcp_d/atlases/atlas-Gordon
 xcp_d/atlases/atlas-Gordon/atlas-Gordon_dseg.json
 xcp_d/atlases/atlas-Gordon/atlas-Gordon_dseg.tsv
-xcp_d/atlases/atlas-Gordon/space-MNIInfant_atlas-Gordon_cohort-1_dseg.nii.gz
+xcp_d/atlases/atlas-Gordon/atlas-Gordon_space-MNIInfant_cohort-1_dseg.nii.gz
 xcp_d/atlases/atlas-HCP
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.json
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.tsv
-xcp_d/atlases/atlas-HCP/space-MNIInfant_atlas-HCP_cohort-1_dseg.nii.gz
+xcp_d/atlases/atlas-HCP/atlas-HCP_space-MNIInfant_cohort-1_dseg.nii.gz
 xcp_d/atlases/atlas-Tian
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.json
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.tsv
-xcp_d/atlases/atlas-Tian/space-MNIInfant_atlas-Tian_cohort-1_dseg.nii.gz
+xcp_d/atlases/atlas-Tian/atlas-Tian_space-MNIInfant_cohort-1_dseg.nii.gz
 xcp_d/dataset_description.json
 xcp_d/desc-linc_qc.json
 xcp_d/logs
@@ -71,151 +72,151 @@ xcp_d/sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_desc-preproc_d
 xcp_d/sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_desc-preproc_design.tsv
 xcp_d/sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_motion.json
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-xcp_d/sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_atlas-4S1056Parcels_cohort-1_alff.tsv
-xcp_d/sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_atlas-4S1056Parcels_cohort-1_coverage.json
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-xcp_d/sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_space-MNIInfant_atlas-4S1056Parcels_cohort-1_measure-pearsoncorrelation_conmat.tsv
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diff --git a/xcp_d/tests/data/test_pnc_cifti_outputs.txt b/xcp_d/tests/data/test_pnc_cifti_outputs.txt
index 6fe8bbe..5920113 100644
--- a/xcp_d/tests/data/test_pnc_cifti_outputs.txt
+++ b/xcp_d/tests/data/test_pnc_cifti_outputs.txt
@@ -1,12 +1,13 @@
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 xcp_d/atlases/atlas-HCP
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.json
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.tsv
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 xcp_d/atlases/atlas-Tian
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.json
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.tsv
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 xcp_d/dataset_description.json
 xcp_d/desc-linc_qc.json
 xcp_d/logs
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 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-rest_acq-singleband_space-fsLR_den-91k_desc-denoisedSmoothed_bold.json
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 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-rest_acq-singleband_space-fsLR_den-91k_desc-denoised_bold.json
 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-rest_acq-singleband_space-fsLR_den-91k_desc-interpolated_bold.dtseries.nii
 xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-rest_acq-singleband_space-fsLR_den-91k_desc-interpolated_bold.json
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 xcp_d/sub-1648798153_ses-PNC1_executive_summary.html
diff --git a/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt b/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt
index de150fc..e9cc4ea 100644
--- a/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt
+++ b/xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt
@@ -1,12 +1,13 @@
 xcp_d/atlases
+xcp_d/atlases/dataset_description.json
 xcp_d/atlases/atlas-4S156Parcels
 xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.json
 xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S156Parcels/space-fsLR_atlas-4S156Parcels_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/atlases/atlas-Glasser
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.json
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.tsv
-xcp_d/atlases/atlas-Glasser/space-fsLR_atlas-Glasser_den-91k_dseg.dlabel.nii
+xcp_d/atlases/atlas-Glasser/atlas-Glasser_space-fsLR_den-91k_dseg.dlabel.nii
 xcp_d/dataset_description.json
 xcp_d/desc-linc_qc.json
 xcp_d/logs
@@ -17,12 +18,12 @@ xcp_d/sub-1648798153/ses-PNC1
 xcp_d/sub-1648798153/ses-PNC1/anat
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@@ -42,49 +43,49 @@ xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_desc-filte
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+xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_space-fsLR_den-91k_stat-alff_desc-smooth_boldmap.dscalar.nii
+xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_space-fsLR_den-91k_stat-alff_desc-smooth_boldmap.json
+xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_space-fsLR_den-91k_stat-reho_boldmap.dscalar.nii
+xcp_d/sub-1648798153/ses-PNC1/func/sub-1648798153_ses-PNC1_task-idemo_space-fsLR_den-91k_stat-reho_boldmap.json
 xcp_d/sub-1648798153_ses-PNC1_executive_summary.html
diff --git a/xcp_d/tests/data/test_ukbiobank_outputs.txt b/xcp_d/tests/data/test_ukbiobank_outputs.txt
index f87b48f..c7021db 100644
--- a/xcp_d/tests/data/test_ukbiobank_outputs.txt
+++ b/xcp_d/tests/data/test_ukbiobank_outputs.txt
@@ -1,60 +1,61 @@
 xcp_d/atlases
+xcp_d/atlases/dataset_description.json
 xcp_d/atlases/atlas-4S1056Parcels
 xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.json
 xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S1056Parcels/space-MNI152NLin6Asym_atlas-4S1056Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S1056Parcels/atlas-4S1056Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-4S156Parcels
 xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.json
 xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S156Parcels/space-MNI152NLin6Asym_atlas-4S156Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S156Parcels/atlas-4S156Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-4S256Parcels
 xcp_d/atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.json
 xcp_d/atlases/atlas-4S256Parcels/atlas-4S256Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S256Parcels/space-MNI152NLin6Asym_atlas-4S256Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S256Parcels/atlas-4S256Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-4S356Parcels
 xcp_d/atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.json
 xcp_d/atlases/atlas-4S356Parcels/atlas-4S356Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S356Parcels/space-MNI152NLin6Asym_atlas-4S356Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S356Parcels/atlas-4S356Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-4S456Parcels
 xcp_d/atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.json
 xcp_d/atlases/atlas-4S456Parcels/atlas-4S456Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S456Parcels/space-MNI152NLin6Asym_atlas-4S456Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S456Parcels/atlas-4S456Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-4S556Parcels
 xcp_d/atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.json
 xcp_d/atlases/atlas-4S556Parcels/atlas-4S556Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S556Parcels/space-MNI152NLin6Asym_atlas-4S556Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S556Parcels/atlas-4S556Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-4S656Parcels
 xcp_d/atlases/atlas-4S656Parcels/atlas-4S656Parcels_dseg.json
 xcp_d/atlases/atlas-4S656Parcels/atlas-4S656Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S656Parcels/space-MNI152NLin6Asym_atlas-4S656Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S656Parcels/atlas-4S656Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-4S756Parcels
 xcp_d/atlases/atlas-4S756Parcels/atlas-4S756Parcels_dseg.json
 xcp_d/atlases/atlas-4S756Parcels/atlas-4S756Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S756Parcels/space-MNI152NLin6Asym_atlas-4S756Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S756Parcels/atlas-4S756Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-4S856Parcels
 xcp_d/atlases/atlas-4S856Parcels/atlas-4S856Parcels_dseg.json
 xcp_d/atlases/atlas-4S856Parcels/atlas-4S856Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S856Parcels/space-MNI152NLin6Asym_atlas-4S856Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S856Parcels/atlas-4S856Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-4S956Parcels
 xcp_d/atlases/atlas-4S956Parcels/atlas-4S956Parcels_dseg.json
 xcp_d/atlases/atlas-4S956Parcels/atlas-4S956Parcels_dseg.tsv
-xcp_d/atlases/atlas-4S956Parcels/space-MNI152NLin6Asym_atlas-4S956Parcels_dseg.nii.gz
+xcp_d/atlases/atlas-4S956Parcels/atlas-4S956Parcels_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-Glasser
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.json
 xcp_d/atlases/atlas-Glasser/atlas-Glasser_dseg.tsv
-xcp_d/atlases/atlas-Glasser/space-MNI152NLin6Asym_atlas-Glasser_dseg.nii.gz
+xcp_d/atlases/atlas-Glasser/atlas-Glasser_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-Gordon
 xcp_d/atlases/atlas-Gordon/atlas-Gordon_dseg.json
 xcp_d/atlases/atlas-Gordon/atlas-Gordon_dseg.tsv
-xcp_d/atlases/atlas-Gordon/space-MNI152NLin6Asym_atlas-Gordon_dseg.nii.gz
+xcp_d/atlases/atlas-Gordon/atlas-Gordon_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-HCP
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.json
 xcp_d/atlases/atlas-HCP/atlas-HCP_dseg.tsv
-xcp_d/atlases/atlas-HCP/space-MNI152NLin6Asym_atlas-HCP_dseg.nii.gz
+xcp_d/atlases/atlas-HCP/atlas-HCP_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/atlases/atlas-Tian
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.json
 xcp_d/atlases/atlas-Tian/atlas-Tian_dseg.tsv
-xcp_d/atlases/atlas-Tian/space-MNI152NLin6Asym_atlas-Tian_dseg.nii.gz
+xcp_d/atlases/atlas-Tian/atlas-Tian_space-MNI152NLin6Asym_dseg.nii.gz
 xcp_d/dataset_description.json
 xcp_d/desc-linc_qc.json
 xcp_d/logs
@@ -72,155 +73,155 @@ xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_desc-preproc_design.j
 xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_desc-preproc_design.tsv
 xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_outliers.json
 xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_outliers.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_alff.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_alff.nii.gz
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_alff.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_alff.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_coverage.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_coverage.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_measure-pearsoncorrelation_conmat.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_measure-pearsoncorrelation_conmat.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_reho.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_reho.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_timeseries.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S1056Parcels_timeseries.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_alff.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_alff.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_coverage.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_coverage.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_measure-pearsoncorrelation_conmat.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_measure-pearsoncorrelation_conmat.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_reho.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_reho.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_timeseries.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S156Parcels_timeseries.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_alff.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_alff.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_coverage.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_coverage.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_measure-pearsoncorrelation_conmat.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_measure-pearsoncorrelation_conmat.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_reho.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_reho.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_timeseries.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S256Parcels_timeseries.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S356Parcels_alff.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S356Parcels_alff.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S356Parcels_coverage.json
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-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S456Parcels_alff.json
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-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S456Parcels_coverage.json
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-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S456Parcels_measure-pearsoncorrelation_conmat.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S456Parcels_measure-pearsoncorrelation_conmat.tsv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S456Parcels_reho.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S456Parcels_reho.tsv
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-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_atlas-4S556Parcels_coverage.tsv
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+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S756Parcels_stat-mean_timeseries.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S756Parcels_stat-mean_timeseries.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-alff_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-alff_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-coverage_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-coverage_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-pearsoncorrelation_relmat.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-pearsoncorrelation_relmat.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-reho_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-reho_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-mean_timeseries.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S856Parcels_stat-mean_timeseries.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-alff_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-alff_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-coverage_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-coverage_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-pearsoncorrelation_relmat.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-pearsoncorrelation_relmat.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-reho_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-reho_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-mean_timeseries.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-4S956Parcels_stat-mean_timeseries.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-alff_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-alff_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-coverage_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-coverage_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-pearsoncorrelation_relmat.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-pearsoncorrelation_relmat.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-reho_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-reho_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-mean_timeseries.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Glasser_stat-mean_timeseries.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-alff_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-alff_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-coverage_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-coverage_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-pearsoncorrelation_relmat.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-pearsoncorrelation_relmat.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-reho_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-reho_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-mean_timeseries.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Gordon_stat-mean_timeseries.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-alff_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-alff_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-coverage_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-coverage_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-pearsoncorrelation_relmat.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-pearsoncorrelation_relmat.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-reho_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-reho_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-mean_timeseries.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-HCP_stat-mean_timeseries.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-alff_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-alff_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-coverage_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-coverage_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-pearsoncorrelation_relmat.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-pearsoncorrelation_relmat.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-reho_bold.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-reho_bold.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-mean_timeseries.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_seg-Tian_stat-mean_timeseries.tsv
 xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_desc-denoisedSmoothed_bold.json
 xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_desc-denoisedSmoothed_bold.nii.gz
 xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_desc-denoised_bold.json
 xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_desc-denoised_bold.nii.gz
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_desc-linc_qc.csv
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_desc-smooth_alff.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_desc-smooth_alff.nii.gz
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_reho.json
-xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_reho.nii.gz
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_desc-linc_qc.tsv
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_stat-alff_desc-smooth_boldmap.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_stat-alff_desc-smooth_boldmap.nii.gz
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_stat-reho_boldmap.json
+xcp_d/sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_space-MNI152NLin6Asym_stat-reho_boldmap.nii.gz
 xcp_d/sub-0000001_ses-01_executive_summary.html
diff --git a/xcp_d/tests/test_interfaces_bids.py b/xcp_d/tests/test_interfaces_bids.py
index 89bf26e..e71b185 100644
--- a/xcp_d/tests/test_interfaces_bids.py
+++ b/xcp_d/tests/test_interfaces_bids.py
@@ -23,7 +23,7 @@ def test_copy_atlas(tmp_path_factory):
     assert os.path.isfile(result.outputs.out_file)
     assert (
         os.path.basename(result.outputs.out_file)
-        == "space-MNI152NLin2009cAsym_atlas-Y_res-2_dseg.nii.gz"
+        == "atlas-Y_space-MNI152NLin2009cAsym_res-2_dseg.nii.gz"
     )
 
     # Check that the NIfTI file raises an error if the resolution varies
@@ -47,7 +47,7 @@ def test_copy_atlas(tmp_path_factory):
     result = copyatlas.run(cwd=tmpdir)
     assert os.path.isfile(result.outputs.out_file)
     assert (
-        os.path.basename(result.outputs.out_file) == "space-fsLR_atlas-Y_den-91k_dseg.dlabel.nii"
+        os.path.basename(result.outputs.out_file) == "atlas-Y_space-fsLR_den-91k_dseg.dlabel.nii"
     )
 
     # TSV
diff --git a/xcp_d/tests/test_utils_bids.py b/xcp_d/tests/test_utils_bids.py
index 3bb7ce9..3b18a32 100644
--- a/xcp_d/tests/test_utils_bids.py
+++ b/xcp_d/tests/test_utils_bids.py
@@ -190,12 +190,17 @@ def test_write_dataset_description(datasets, tmp_path_factory, caplog):
 
     # The function expects a description file in the fmri_dir.
     with pytest.raises(FileNotFoundError, match="Dataset description DNE"):
-        xbids.write_dataset_description(tmpdir, tmpdir)
+        xbids.write_dataset_description(tmpdir, tmpdir, atlases=None, custom_confounds_folder=None)
     assert not os.path.isfile(dset_description)
 
     # It will work when we give it a real fmri_dir.
     fmri_dir = datasets["ds001419"]
-    xbids.write_dataset_description(fmri_dir, tmpdir, custom_confounds_folder="/fake/path4")
+    xbids.write_dataset_description(
+        fmri_dir,
+        tmpdir,
+        atlases=["Gordon"],
+        custom_confounds_folder="/fake/path4",
+    )
     assert os.path.isfile(dset_description)
 
     # Now overwrite the description.
@@ -204,7 +209,12 @@ def test_write_dataset_description(datasets, tmp_path_factory, caplog):
 
     assert "'preprocessed' is already a dataset link" not in caplog.text
     assert "'custom_confounds' is already a dataset link" not in caplog.text
-    xbids.write_dataset_description(tmpdir, tmpdir, custom_confounds_folder="/fake/path4")
+    xbids.write_dataset_description(
+        tmpdir,
+        tmpdir,
+        atlases=["Gordon"],
+        custom_confounds_folder="/fake/path4",
+    )
     assert "'preprocessed' is already a dataset link" in caplog.text
     assert "'custom_confounds' is already a dataset link" in caplog.text
 
@@ -214,7 +224,49 @@ def test_write_dataset_description(datasets, tmp_path_factory, caplog):
         json.dump(desc, fo, indent=4)
 
     assert "Previous output generated by version" not in caplog.text
-    xbids.write_dataset_description(fmri_dir, tmpdir)
+    xbids.write_dataset_description(fmri_dir, tmpdir, atlases=None, custom_confounds_folder=None)
+    assert "Previous output generated by version" in caplog.text
+
+    # Should raise a warning if DatasetType is not in the description
+    desc.pop("DatasetType")
+    with open(dset_description, "w") as fo:
+        json.dump(desc, fo, indent=4)
+
+    assert "DatasetType key not in" not in caplog.text
+    xbids.write_dataset_description(tmpdir, tmpdir, atlases=None, custom_confounds_folder=None)
+    assert "DatasetType key not in" in caplog.text
+
+    # Should raise an error if DatasetType is present, but isn't "derivative"
+    desc["DatasetType"] = "raw"
+    with open(dset_description, "w") as fo:
+        json.dump(desc, fo, indent=4)
+
+    with pytest.raises(ValueError, match="XCP-D only works on derivative datasets."):
+        xbids.write_dataset_description(
+            tmpdir,
+            tmpdir,
+            atlases=None,
+            custom_confounds_folder=None,
+        )
+
+
+def test_write_atlas_dataset_description(tmp_path_factory, caplog):
+    """Test write_atlas_dataset_description."""
+    tmpdir = tmp_path_factory.mktemp("test_write_atlas_dataset_description")
+    dset_description = os.path.join(tmpdir, "dataset_description.json")
+    xbids.write_atlas_dataset_description(tmpdir)
+    assert os.path.isfile(dset_description)
+
+    # Now change the version and re-run the function.
+    with open(dset_description, "r") as fo:
+        desc = json.load(fo)
+
+    desc["GeneratedBy"][0]["Version"] = "0.0.1"
+    with open(dset_description, "w") as fo:
+        json.dump(desc, fo, indent=4)
+
+    assert "Previous output generated by version" not in caplog.text
+    xbids.write_atlas_dataset_description(tmpdir)
     assert "Previous output generated by version" in caplog.text
 
 
@@ -364,6 +416,16 @@ def test_make_xcpd_uri():
     assert uri == ["bids::sub-01/func/sub-01_task-rest_bold.nii.gz"]
 
 
+def test_make_atlas_uri():
+    """Test _make_atlas_uri."""
+    out_file = "/path/to/dset/xcp_d/atlases/sub-01/func/sub-01_task-rest_bold.nii.gz"
+    uri = xbids._make_atlas_uri(out_file, output_dir="/path/to/dset")
+    assert uri == ["bids:atlas:sub-01/func/sub-01_task-rest_bold.nii.gz"]
+
+    xbids._make_atlas_uri([out_file], output_dir="/path/to/dset")
+    assert uri == ["bids:atlas:sub-01/func/sub-01_task-rest_bold.nii.gz"]
+
+
 def test_make_xcpd_uri_lol():
     """Test _make_xcpd_uri_lol."""
     in_list = [