Merge tag '1.3.0' into halfpipe

1.3.0

First release in the 1.3.x series.
This release includes enhancements and bug-fixes towards the release of the first
LTS (*long-term support*) 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: Upstream all bug-fixes in the 1.2.9 release
* MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (nipreps#550)
* MAINT: Update to Python +3.6 (nipreps#541)

Author: HippocampusGirl

CHANGES.rst

@@ -1,24 +1,34 @@
-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
+1.3.0 (September 11, 2020)
+==========================
+First release in the 1.3.x series.
+This release includes enhancements and bug-fixes towards the release of the first 
+LTS (*long-term support*) 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)
+* 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: Upstream all bug-fixes in the 1.2.9 release
+* MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (#550)
+* MAINT: Update to Python +3.6 (#541)
+
+1.2.9 (September 11, 2020)
+==========================
+Bug-fix release in the 1.2.x series with very minor problems addressed.
+
+* FIX: Reportlets would crash in edge condition (#566)
+* FIX: AROMA metadata ``CsfFraction`` -> ``CSFFraction`` (#563)
+* FIX: Add DWI nonstandard spaces (#565)
 
 1.2.8 (September 03, 2020)
 ==========================

niworkflows/interfaces/utils.py

@@ -967,7 +967,7 @@ def less_breakable(a_string):
             for i in tsv_data.index
         ]
         tsv_data.columns = [
-            re.sub(re_to_camel, camel, less_breakable(i).title(), 0)
+            re.sub(re_to_camel, camel, less_breakable(i).title(), 0).replace("Csf", "CSF")
             for i in tsv_data.columns
         ]
     json_data = tsv_data.to_json(orient="index")

niworkflows/utils/spaces.py

@@ -14,6 +14,8 @@
     "run",
     "sbref",
     "session",
+    "individual",
+    "dwi",
 ]
 """List of supported nonstandard reference spaces."""
 

niworkflows/viz/utils.py

@@ -175,7 +175,7 @@ def cuts_from_bbox(mask_nii, cuts=3):
         smin, smax = (0, mask_data.shape[ax] - 1)
 
         B = np.argwhere(c > th)
-        if not B.size:  # Threshold too high
+        if B.size < cuts:  # Threshold too high
             B = np.argwhere(c > 0)
         if B.size:
             smin, smax = B.min(), B.max()