Merge tag '1.3.0rc3' into halfpipe

1.3.0rc3

First release in the 1.3.x series. This release includes enhancements and bug-fixes
towards the release of the first LTS version of fMRIPrep.
PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces
have been deemed ready to upstream into Nipype, and several improvements regarding
multi-echo EPI are included.
With thanks to Basile Pinsard for contributions.

* FIX: Patch ``ApplyTransforms`` spec to permit identity in a chain (nipreps#554)
* FIX: Add dots to extensions in PyBIDS' config file (nipreps#548)
* FIX: Segmentation plots aligned with cardinal axes (nipreps#544)
* FIX: Skip T1w file existence check if ``anat_derivatives`` are provided (nipreps#545)
* FIX: Avoid diverting CIFTI dtype from original BOLD (nipreps#532)
* ENH: Add ``smooth`` input to ``RegridToZooms`` (nipreps#549)
* ENH: Enable ``DerivativesDataSink`` to take multiple source files to derive entities (nipreps#547)
* ENH: Allow ``bold_reference_wf`` to accept multiple EPIs/SBRefs (nipreps#408)
* ENH: Numerical stability of EPI brain-masks using probabilistic prior (nipreps#485)
* ENH: Add a pure-Python interface to resample to specific resolutions (nipreps#511)
* MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (nipreps#550)
* MAINT: Update to Python +3.6 (nipreps#541)

Author: HippocampusGirl

.circleci/config.yml

@@ -151,8 +151,8 @@ jobs:
     steps:
       - restore_cache:
           keys:
-            - regression-v2-{{ .Revision }}
-            - regression-v2-
+            - regression-v5-{{ .Revision }}
+            - regression-v5-
       - run:
           name: Get truncated BOLD series
           command: |
@@ -175,7 +175,7 @@ jobs:
               echo "Pre-computed masks were cached"
             fi
       - save_cache:
-         key: regression-v2-{{ .Revision }}-{{ epoch }}
+         key: regression-v5-{{ .Revision }}-{{ epoch }}
          paths:
             - /tmp/data
 
@@ -284,13 +284,13 @@ jobs:
 
       - restore_cache:
           keys:
-            - regression-v2-{{ .Revision }}
+            - regression-v5-{{ .Revision }}
       - restore_cache:
           keys:
-            - masks-workdir-v1-{{ .Branch }}-{{epoch}}
-            - masks-workdir-v1-{{ .Branch }}-
-            - masks-workdir-v1-master-
-            - masks-workdir-v1-
+            - masks-workdir-v3-{{ .Branch }}-{{epoch}}
+            - masks-workdir-v3-{{ .Branch }}-
+            - masks-workdir-v3-master-
+            - masks-workdir-v3-
       - run:
           name: Run regression tests on EPI masks
           no_output_timeout: 2h
@@ -307,14 +307,22 @@ jobs:
               coverage run -p --rcfile=setup.cfg \
                      -m pytest --junit-xml=/tmp/masks/reports/regression.xml \
                      niworkflows/func/tests/
-      - save_cache:
-         key: masks-workdir-v1-{{ .Branch }}-{{ epoch }}
-         paths:
-            - /tmp/masks/workdir
+      - run:
+          name: Clear reports folder & delete plot generator cache
+          command: |
+            pushd reports/
+            tar cvfz fmriprep_bold_mask.tar.gz fmriprep_bold_mask/*/*.nii.gz
+            rm -rf /tmp/masks/reports/fmriprep_bold_mask/
+            popd
+            find workdir/ -name "mask_diff_plot" -exec rm -rf {} +
       - store_artifacts:
           path: /tmp/masks/reports
       - store_test_results:
           path: /tmp/masks/reports
+      - save_cache:
+         key: masks-workdir-v3-{{ .Branch }}-{{ epoch }}
+         paths:
+            - /tmp/masks/workdir
 
       - run:
           name: Coverage preparation
@@ -339,15 +347,6 @@ jobs:
             cp /tmp/masks/reports/coverage.xml .
             sed -i "s+/src/niworkflows+/tmp/src/niworkflows+g" coverage.xml
             python -m codecov --file coverage.xml --flags masks -e CIRCLE_JOB
-      - run:
-          name: Package new masks
-          when: always
-          no_output_timeout: 10m
-          working_directory: /tmp/data
-          command: |
-            tar cfz /tmp/masks/fmriprep_bold_mask.tar.gz fmriprep_bold_mask/*/*.nii.gz
-      - store_artifacts:
-          path: /tmp/masks/fmriprep_bold_mask.tar.gz
 
   test_package:
     machine:

CHANGES.rst

@@ -1,3 +1,38 @@
+1.3.0 (TBD)
+===========
+First release in the 1.3.x series. This release includes enhancements and bug-fixes
+towards the release of the first LTS version of fMRIPrep.
+PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces
+have been deemed ready to upstream into Nipype, and several improvements regarding
+multi-echo EPI are included.
+With thanks to Basile Pinsard for contributions.
+
+  * FIX: Patch ``ApplyTransforms`` spec to permit identity in a chain (#554)
+  * FIX: Add dots to extensions in PyBIDS' config file (#548)
+  * FIX: Segmentation plots aligned with cardinal axes (#544)
+  * FIX: Skip T1w file existence check if ``anat_derivatives`` are provided (#545)
+  * FIX: Avoid diverting CIFTI dtype from original BOLD (#532)
+  * ENH: Add ``smooth`` input to ``RegridToZooms`` (#549)
+  * ENH: Enable ``DerivativesDataSink`` to take multiple source files to derive entities (#547)
+  * ENH: Allow ``bold_reference_wf`` to accept multiple EPIs/SBRefs (#408)
+  * ENH: Numerical stability of EPI brain-masks using probabilistic prior (#485)
+  * ENH: Add a pure-Python interface to resample to specific resolutions (#511)
+  * MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (#550)
+  * MAINT: Update to Python +3.6 (#541)
+
+1.2.8 (September 03, 2020)
+==========================
+Bug-fix release in the 1.2.x series with a minor improvement of the correlations plot.
+
+* FIX: Improved control over correlations plot (#561)
+
+1.2.7 (August 12, 2020)
+=======================
+Bug-fix release in the 1.2.x series with a very minor improvement of the reportlets.
+
+* FIX: Pin PyBIDS < 0.11 (and TemplateFlow < 0.6.3) only on the 1.2.x series. (#552)
+* FIX: Use ``numpy.linspace`` to calculate mosaic plots' cutting planes (#543)
+
 1.2.6 (June 09, 2020)
 =====================
 Bug-fix release in the 1.2.x series addressing minor bugs encountered mostly

docs/requirements.txt

@@ -1,7 +1,7 @@
 git+https://github.com/AleksandarPetrov/napoleon.git@0dc3f28a309ad602be5f44a9049785a1026451b3#egg=sphinxcontrib-napoleon
 git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398feff05344051bbce0f63#egg=sphinxcontrib-versioning
 nbsphinx
-nipype>=1.3.1
+git+https://github.com/nipy/nipype.git@master#egg=nipype
 nitransforms >= 20.0.0rc3,<20.2
 packaging
 pydot>=1.2.3

niworkflows/anat/ants.py

@@ -13,17 +13,20 @@
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
 from nipype.interfaces.fsl.maths import ApplyMask
-from nipype.interfaces.ants import N4BiasFieldCorrection, Atropos, MultiplyImages
-
-from ..utils.misc import get_template_specs
-
-# niworkflows
-from ..interfaces.ants import (
+from nipype.interfaces.ants import (
+    AI,
+    Atropos,
     ImageMath,
+    MultiplyImages,
+    N4BiasFieldCorrection,
     ResampleImageBySpacing,
-    AI,
     ThresholdImage,
 )
+
+from ..utils.misc import get_template_specs
+from ..utils.connections import pop_file as _pop
+
+# niworkflows
 from ..interfaces.fixes import (
     FixHeaderRegistration as Registration,
     FixHeaderApplyTransforms as ApplyTransforms,
@@ -897,12 +900,6 @@ def init_n4_only_wf(
     return wf
 
 
-def _pop(in_files):
-    if isinstance(in_files, (list, tuple)):
-        return in_files[0]
-    return in_files
-
-
 def _select_labels(in_segm, labels):
     from os import getcwd
     import numpy as np

niworkflows/data/nipreps.json

@@ -75,7 +75,7 @@
     },
     {
       "name": "extension",
-      "pattern": "[._]*[a-zA-Z0-9]*?\\.([^/\\\\]+)$"
+      "pattern": "[._]*[a-zA-Z0-9]*?(\\.[^/\\\\]+)$"
     },
     {
       "name": "atlas",
@@ -132,25 +132,25 @@
     }
   ],
   "default_path_patterns": [
-    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_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}][_cohort-{cohort}][_den-{density}]_hemi-{hemi<L|R>}_{suffix<wm|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat>}.{extension<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}][_res-{resolution}]_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}][_res-{resolution}]_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-{resolution}][_desc-{desc}]_{suffix<bold|cbv|phase|sbref|boldref|dseg>}.{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}][_cohort-{cohort}][_res-{resolution}]_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}][_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}][_cohort-{cohort}][_desc-{desc}]_{suffix<regressors>|regressors}.{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}][_desc-{desc}]_{suffix<components|mixing>|components}.{extension<json|tsv|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}][_cohort-{cohort}][_desc-{desc}]_{suffix<decomposition>|decomposition}.{extension<json>|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-{density}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<bold>}.{extension<dtseries.nii|dtseries.json|func.gii|func.json>}",
-    "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi|epiref|lowb|dseg>}.{extension<json|nii.gz|nii>|nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>}.{extension<json|nii.gz|nii>|nii.gz}",
-    "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi>}.{extension<tsv|bval|bvec>|tsv}",
-    "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<fieldmap>}.{extension<nii|nii.gz|json>|nii.gz}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_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>}",
-    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}.{extension<html|svg>}",
-    "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>}.{extension<html|svg>}"
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_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}][_cohort-{cohort}][_den-{density}]_hemi-{hemi<L|R>}_{suffix<wm|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat>}{extension<.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}][_res-{resolution}]_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}][_res-{resolution}]_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-{resolution}][_desc-{desc}]_{suffix<bold|cbv|phase|sbref|boldref|dseg>}{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}][_cohort-{cohort}][_res-{resolution}]_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}][_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}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries|regressors>|timeseries}{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}][_desc-{desc}]_{suffix<components|mixing>|components}{extension<.json|.tsv|.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}][_cohort-{cohort}][_desc-{desc}]_{suffix<decomposition>|decomposition}{extension<.json>|.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-{density}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<bold>}{extension<.dtseries.nii|.dtseries.json|.func.gii|.func.json>}",
+    "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi|epiref|lowb|dseg>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi>}{extension<.tsv|.bval|.bvec>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_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>}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg>}",
+    "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>}{extension<.html|.svg>}"
   ]
 }