Skip to content

Commit

Permalink
Merge remote-tracking branch 'upstream/maint/0.13.x'
Browse files Browse the repository at this point in the history
  • Loading branch information
effigies committed Dec 8, 2023
2 parents 07e5327 + 0136f1b commit 3be9ce1
Show file tree
Hide file tree
Showing 3 changed files with 186 additions and 0 deletions.
16 changes: 16 additions & 0 deletions CHANGES.rst
Original file line number Diff line number Diff line change
@@ -1,3 +1,19 @@
0.13.2 (December 08, 2023)
==========================
Bug fix release in the 0.13.x series.

This release fixes a check for skull-stripping in auto mode, and adds
missing fsLR atlases to the Python package resources.
The Docker image has also been updated to ensure FreeSurfer can be run
from the sMRIPrep container.

With thanks to Patrick Sadil for reports and fixes.

* ENH: Add 59k atlases (#405)
* FIX: Repair FreeSurfer dependency in Dockerfile (tcsh) (#404)
* FIX: Invert result of skull-strip check in auto mode (#402)


0.13.1 (November 21, 2023)
==========================
Bug fix release in the 0.13.x series.
Expand Down
85 changes: 85 additions & 0 deletions smriprep/data/atlases/L.atlasroi.59k_fs_LR.shape.gii
Original file line number Diff line number Diff line change
@@ -0,0 +1,85 @@
<?xml version="1.0" encoding="UTF-8"?>
<GIFTI xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd"
Version="1"
NumberOfDataArrays="1">
<MetaData>
<MD>
<Name><![CDATA[AnatomicalStructurePrimary]]></Name>
<Value><![CDATA[CortexLeft]]></Value>
</MD>
<MD>
<Name><![CDATA[ParentProvenance]]></Name>
<Value><![CDATA[/media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/L.sphere.60k_fs_LR.surf.gii:
/home/brainmappers/workbench/fetchdir/wb_command.3496 -surface-flip-lr /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/R.sphere.60k_fs_LR.surf.gii /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/L.sphere.60k_fs_LR.surf.gii
]]></Value>
</MD>
<MD>
<Name><![CDATA[ProgramProvenance]]></Name>
<Value><![CDATA[Connectome Workbench
Type: Command Line Application
Version: 1.0
Qt Compiled Version: 4.8.5
Qt Runtime Version: 4.8.1
commit: d657b42378a5f8b9946611d5bda5750c16106c08
commit date: 2014-12-10 22:27:53 -0600
Compiler: c++ (/usr/bin)
Compiler Version:
Compiled Debug: NO
Operating System: Linux
]]></Value>
</MD>
<MD>
<Name><![CDATA[Provenance]]></Name>
<Value><![CDATA[/home/brainmappers/workbench/fetchdir/wb_command.3509 -metric-resample /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/L.atlasroi.164k_fs_LR.shape.gii /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/fsaverage.L_LR.spherical_std.164k_fs_LR.surf.gii /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/L.sphere.60k_fs_LR.surf.gii BARYCENTRIC /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/L.atlasroi.60k_fs_LR.shape.gii -largest]]></Value>
</MD>
<MD>
<Name><![CDATA[WorkingDirectory]]></Name>
<Value><![CDATA[/media/myelin/brainmappers/HardDrives/2TBB/Connectome_Project/Pipelines]]></Value>
</MD>
</MetaData>
<LabelTable>
<Label Key="0" Red="1" Green="1" Blue="1" Alpha="0"><![CDATA[???]]></Label>
</LabelTable>
<DataArray Intent="NIFTI_INTENT_NORMAL"
DataType="NIFTI_TYPE_FLOAT32"
ArrayIndexingOrder="RowMajorOrder"
Dimensionality="1"
Dim0="59292"
Encoding="GZipBase64Binary"
Endian="LittleEndian"
ExternalFileName=""
ExternalFileOffset="0">
<MetaData>
<MD>
<Name><![CDATA[Name]]></Name>
<Value><![CDATA[Atlas_Cortex_ROI]]></Value>
</MD>
<MD>
<Name><![CDATA[PaletteColorMapping]]></Name>
<Value><![CDATA[<PaletteColorMapping Version="1">
<ScaleMode>MODE_AUTO_SCALE_PERCENTAGE</ScaleMode>
<AutoScalePercentageValues>98.000000 2.000000 2.000000 98.000000</AutoScalePercentageValues>
<UserScaleValues>-100.000000 0.000000 0.000000 100.000000</UserScaleValues>
<PaletteName>ROY-BIG-BL</PaletteName>
<InterpolatePalette>true</InterpolatePalette>
<DisplayPositiveData>true</DisplayPositiveData>
<DisplayZeroData>false</DisplayZeroData>
<DisplayNegativeData>true</DisplayNegativeData>
<ThresholdTest>THRESHOLD_TEST_SHOW_OUTSIDE</ThresholdTest>
<ThresholdType>THRESHOLD_TYPE_OFF</ThresholdType>
<ThresholdFailureInGreen>false</ThresholdFailureInGreen>
<ThresholdNormalValues>-1.000000 1.000000</ThresholdNormalValues>
<ThresholdMappedValues>-1.000000 1.000000</ThresholdMappedValues>
<ThresholdMappedAvgAreaValues>-1.000000 1.000000</ThresholdMappedAvgAreaValues>
<ThresholdDataName></ThresholdDataName>
<ThresholdRangeMode>PALETTE_THRESHOLD_RANGE_MODE_MAP</ThresholdRangeMode>
<ThresholdLowHighLinked>false</ThresholdLowHighLinked>
</PaletteColorMapping>
]]></Value>
</MD>
</MetaData>
<Data>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</Data>
</DataArray>
</GIFTI>
85 changes: 85 additions & 0 deletions smriprep/data/atlases/R.atlasroi.59k_fs_LR.shape.gii
Original file line number Diff line number Diff line change
@@ -0,0 +1,85 @@
<?xml version="1.0" encoding="UTF-8"?>
<GIFTI xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="http://brainvis.wustl.edu/caret6/xml_schemas/GIFTI_Caret.xsd"
Version="1"
NumberOfDataArrays="1">
<MetaData>
<MD>
<Name><![CDATA[AnatomicalStructurePrimary]]></Name>
<Value><![CDATA[CortexRight]]></Value>
</MD>
<MD>
<Name><![CDATA[ParentProvenance]]></Name>
<Value><![CDATA[/media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/R.sphere.60k_fs_LR.surf.gii:
/home/brainmappers/workbench/fetchdir/wb_command.3492 -surface-create-sphere 60000 /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/R.sphere.60k_fs_LR.surf.gii
]]></Value>
</MD>
<MD>
<Name><![CDATA[ProgramProvenance]]></Name>
<Value><![CDATA[Connectome Workbench
Type: Command Line Application
Version: 1.0
Qt Compiled Version: 4.8.5
Qt Runtime Version: 4.8.1
commit: d657b42378a5f8b9946611d5bda5750c16106c08
commit date: 2014-12-10 22:27:53 -0600
Compiler: c++ (/usr/bin)
Compiler Version:
Compiled Debug: NO
Operating System: Linux
]]></Value>
</MD>
<MD>
<Name><![CDATA[Provenance]]></Name>
<Value><![CDATA[/home/brainmappers/workbench/fetchdir/wb_command.3539 -metric-resample /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/R.atlasroi.164k_fs_LR.shape.gii /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/fsaverage.R_LR.spherical_std.164k_fs_LR.surf.gii /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/R.sphere.60k_fs_LR.surf.gii BARYCENTRIC /media/2TBB/Connectome_Project/Pipelines/global/templates/standard_mesh_atlases/R.atlasroi.60k_fs_LR.shape.gii -largest]]></Value>
</MD>
<MD>
<Name><![CDATA[WorkingDirectory]]></Name>
<Value><![CDATA[/media/myelin/brainmappers/HardDrives/2TBB/Connectome_Project/Pipelines]]></Value>
</MD>
</MetaData>
<LabelTable>
<Label Key="0" Red="1" Green="1" Blue="1" Alpha="0"><![CDATA[???]]></Label>
</LabelTable>
<DataArray Intent="NIFTI_INTENT_NORMAL"
DataType="NIFTI_TYPE_FLOAT32"
ArrayIndexingOrder="RowMajorOrder"
Dimensionality="1"
Dim0="59292"
Encoding="GZipBase64Binary"
Endian="LittleEndian"
ExternalFileName=""
ExternalFileOffset="0">
<MetaData>
<MD>
<Name><![CDATA[Name]]></Name>
<Value><![CDATA[Atlas_Cortex_ROI]]></Value>
</MD>
<MD>
<Name><![CDATA[PaletteColorMapping]]></Name>
<Value><![CDATA[<PaletteColorMapping Version="1">
<ScaleMode>MODE_AUTO_SCALE_PERCENTAGE</ScaleMode>
<AutoScalePercentageValues>98.000000 2.000000 2.000000 98.000000</AutoScalePercentageValues>
<UserScaleValues>-100.000000 0.000000 0.000000 100.000000</UserScaleValues>
<PaletteName>ROY-BIG-BL</PaletteName>
<InterpolatePalette>true</InterpolatePalette>
<DisplayPositiveData>true</DisplayPositiveData>
<DisplayZeroData>false</DisplayZeroData>
<DisplayNegativeData>true</DisplayNegativeData>
<ThresholdTest>THRESHOLD_TEST_SHOW_OUTSIDE</ThresholdTest>
<ThresholdType>THRESHOLD_TYPE_OFF</ThresholdType>
<ThresholdFailureInGreen>false</ThresholdFailureInGreen>
<ThresholdNormalValues>-1.000000 1.000000</ThresholdNormalValues>
<ThresholdMappedValues>-1.000000 1.000000</ThresholdMappedValues>
<ThresholdMappedAvgAreaValues>-1.000000 1.000000</ThresholdMappedAvgAreaValues>
<ThresholdDataName></ThresholdDataName>
<ThresholdRangeMode>PALETTE_THRESHOLD_RANGE_MODE_MAP</ThresholdRangeMode>
<ThresholdLowHighLinked>false</ThresholdLowHighLinked>
</PaletteColorMapping>
]]></Value>
</MD>
</MetaData>
<Data>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</Data>
</DataArray>
</GIFTI>

0 comments on commit 3be9ce1

Please sign in to comment.