From a67e64eccb8e0121e774b7a3b3ae4d5cb09efcf8 Mon Sep 17 00:00:00 2001
From: Andrey Fedorov <andrey.fedorov@gmail.com>
Date: Mon, 22 Apr 2024 15:54:11 -0400
Subject: [PATCH 1/3] allow saving merged segments to all formats

I do not see a reason to restrict this feature to NRRD
---
 apps/seg/segimage2itkimage.cxx | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/apps/seg/segimage2itkimage.cxx b/apps/seg/segimage2itkimage.cxx
index 487cb543..31dce197 100644
--- a/apps/seg/segimage2itkimage.cxx
+++ b/apps/seg/segimage2itkimage.cxx
@@ -25,11 +25,6 @@ int main(int argc, char *argv[])
     dcmtk::log4cplus::BasicConfigurator::doConfigure();
   }
 
-  if (mergeSegments && outputType != "nrrd") {
-    std::cerr << "ERROR: mergeSegments option is only supported when output format is NRRD!" << std::endl;
-    return EXIT_FAILURE;
-  }
-
   if(helper::isUndefinedOrPathDoesNotExist(inputSEGFileName, "Input DICOM file")
      || helper::isUndefinedOrPathDoesNotExist(outputDirName, "Output directory"))
     return EXIT_FAILURE;

From c7825749de83371d0f1d1e7a45d84a0bcf190ba3 Mon Sep 17 00:00:00 2001
From: Andrey Fedorov <andrey.fedorov@gmail.com>
Date: Mon, 22 Apr 2024 21:52:26 -0400
Subject: [PATCH 2/3] update python to 3.10.11

3.7.14 appears to be no longer available, and 3.10.11 is the next one available based on https://raw.githubusercontent.com/actions/python-versions/main/versions-manifest.json
---
 .github/workflows/cmake-macos.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cmake-macos.yml b/.github/workflows/cmake-macos.yml
index f2f4380c..afbe1c29 100644
--- a/.github/workflows/cmake-macos.yml
+++ b/.github/workflows/cmake-macos.yml
@@ -24,7 +24,7 @@ jobs:
         fetch-tags: true     
     - uses: actions/setup-python@v4
       with:
-        python-version: '3.7.14'
+        python-version: '3.10.11'
 
     # Install build tools (cmake and ninja) as well as jsondiff
     - name: "Install jsondiff"
@@ -119,4 +119,4 @@ jobs:
         --prerelease-packages ${{ github.workspace }}/dcmqi-build/dcmqi-build/dcmqi-*-mac-*.tar.gz \
         --prerelease-packages-clear-pattern "dcmqi-*-mac-*" \
         --prerelease-packages-keep-pattern "*<COMMIT_DATE>-<COMMIT_SHORT_SHA>*" \
-        --exit-success-if-missing-token --token ${{ secrets.GA_TOKEN }}
\ No newline at end of file
+        --exit-success-if-missing-token --token ${{ secrets.GA_TOKEN }}

From c0bef7a0472d68ab6da623cff16bf99fb7d01889 Mon Sep 17 00:00:00 2001
From: Andrey Fedorov <andrey.fedorov@gmail.com>
Date: Tue, 23 Apr 2024 07:09:04 -0400
Subject: [PATCH 3/3] remove incorrect statement re 4D NRRD output

---
 apps/seg/segimage2itkimage.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apps/seg/segimage2itkimage.xml b/apps/seg/segimage2itkimage.xml
index af3a72ea..0fbc7bae 100644
--- a/apps/seg/segimage2itkimage.xml
+++ b/apps/seg/segimage2itkimage.xml
@@ -72,7 +72,7 @@
       <channel>input</channel>
       <longflag>mergeSegments</longflag>
       <default>false</default>
-      <description>Save all segments into a single file. When segments are non-overlapping, output is a single 3D file. If overlapping, single 4D following conventions of 3D Slicer segmentations format. Only supported when the output is NRRD for now.</description>
+      <description>Save all segments into a single file. When segments are non-overlapping, output is a single 3D file. If overlapping segments are identified, multiple 3D files will be created each containing non-overlapping segments. Metadata JSON files will be created for each such 3D file.</description>
     </boolean>
 
   </parameters>