Merge master

shimming-toolbox · Dec 21, 2023 · c601ace · c601ace
2 parents 29d0526 + 9a1671d
commit c601ace
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Showing 3 changed files with 36 additions and 8 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -19,8 +19,8 @@ jobs:
     strategy:
       matrix:
         os:
-          - 'macos-11'
           - 'macos-12'
+          - 'macos-13'
           - 'ubuntu-22.04'
           - 'ubuntu-20.04'
         python-version:
@@ -33,10 +33,6 @@ jobs:
           echo $HOME
       - uses: actions/checkout@v3
 
-      - name: Set XCode version
-        if: contains(matrix.os, 'macos-11.0')
-        run: sudo xcode-select -s "/Applications/Xcode_12.2.app"
-
       - name: Set up Python
         uses: actions/setup-python@v2
         with:

diff --git a/config/dcm2bids.json b/config/dcm2bids.json
@@ -94,6 +94,38 @@
                 "ImageType": [".*", ".*", "M", ".*", "UNI"]
             }
         },
+        {
+            "datatype": "anat",
+            "suffix": "inv-1_MP2RAGE",
+            "criteria": {
+                "Manufacturer": "Siemens",
+                "SequenceName": ".*tfl3d1_16.*",
+                "ProtocolName": ".*mp2rage.*",
+                "SeriesDescription": ".*_INV1",
+                "ImageType": [".*", ".*", "M", "NORM", ".*"]
+            }
+        },
+        {
+            "datatype": "anat",
+            "suffix": "inv-2_MP2RAGE",
+            "criteria": {
+                "Manufacturer": "Siemens",
+                "SequenceName": ".*tfl3d1_16.*",
+                "ProtocolName": ".*mp2rage.*",
+                "SeriesDescription": ".*_INV2",
+                "ImageType": [".*", ".*", "M", "NORM", ".*"]
+            }
+        },
+        {
+            "datatype": "anat",
+            "suffix": "UNIT1",
+            "criteria": {
+                "Manufacturer": "Siemens",
+                "SequenceName": ".*tfl3d1_16.*",
+                "ProtocolName": ".*mp2rage.*",
+                "ImageType": [".*", ".*", "M", "UNI", ".*"]
+            }
+        },
         {
             "datatype": "anat",
             "suffix": "T1w",

diff --git a/shimmingtoolbox/dicom_to_nifti.py b/shimmingtoolbox/dicom_to_nifti.py
@@ -125,11 +125,11 @@ def rename_phasediff(path_nifti, subject_id):
             # Open the json file
             with open(fname_json) as json_file:
                 json_data = json.load(json_file)
-                # Make sure it is a phase data and that the keys EchoTime1 and EchoTime2 are defined and that
-                # sequenceName's last digit is 2 (refers to number of echoes when using dcm2bids)
+                # Make sure it is phase data and that the keys EchoTime1 and EchoTime2 are defined and that
+                # the tag "sequenceName" includes fm2d2 which is Siemens' sequence that outputs a phasediff
                 if ('ImageType' in json_data) and ('P' in json_data['ImageType']) and \
                    ('EchoTime1' in json_data) and ('EchoTime2' in json_data) and \
-                   ('SequenceName' in json_data) and (int(json_data['SequenceName'][-1]) == 2) and \
+                   ('SequenceName' in json_data) and ('fm2d2' in json_data['SequenceName']) and \
                    ('EchoNumber' in json_data) and (int(json_data['EchoNumber']) == 2):
                     # Make sure it is not already named phasediff
                     if len(os.path.basename(fname_json).split(subject_id, 1)[-1].rsplit('phasediff', 1)) == 1: