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FIX: Conditionally drop derived volumes from DWI sequences #1296

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merged 3 commits into from
Feb 27, 2024
Merged

FIX: Conditionally drop derived volumes from DWI sequences #1296

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4b65364
DATA: Add dcm_qa_xa30 as submodule for test data
effigies Feb 8, 2024
bc227ec
TEST: Add test for Siemens TRACE volume
effigies Feb 22, 2024
3f81a96
FIX: Conditionally drop isotropic frames
effigies Feb 22, 2024
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3 changes: 3 additions & 0 deletions .gitmodules
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Original file line number Diff line number Diff line change
Expand Up @@ -19,3 +19,6 @@
[submodule "nibabel-data/nitest-dicom"]
path = nibabel-data/nitest-dicom
url = https://github.com/effigies/nitest-dicom
[submodule "nibabel-data/dcm_qa_xa30"]
path = nibabel-data/dcm_qa_xa30
url = https://github.com/neurolabusc/dcm_qa_xa30.git
1 change: 1 addition & 0 deletions nibabel-data/dcm_qa_xa30
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Submodule dcm_qa_xa30 added at 89b250
5 changes: 4 additions & 1 deletion nibabel/nicom/dicomwrappers.py
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Expand Up @@ -509,11 +509,14 @@ def image_shape(self):
if hasattr(first_frame, 'get') and first_frame.get([0x18, 0x9117]):
# DWI image may include derived isotropic, ADC or trace volume
try:
self.frames = pydicom.Sequence(
anisotropic = pydicom.Sequence(
frame
for frame in self.frames
if frame.MRDiffusionSequence[0].DiffusionDirectionality != 'ISOTROPIC'
)
# Image contains DWI volumes followed by derived images; remove derived images
if len(anisotropic) != 0:
self.frames = anisotropic
except IndexError:
# Sequence tag is found but missing items!
raise WrapperError('Diffusion file missing information')
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12 changes: 12 additions & 0 deletions nibabel/nicom/tests/test_dicomwrappers.py
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Expand Up @@ -35,6 +35,11 @@
DATA_FILE_EMPTY_ST = pjoin(IO_DATA_PATH, 'slicethickness_empty_string.dcm')
DATA_FILE_4D_DERIVED = pjoin(get_nibabel_data(), 'nitest-dicom', '4d_multiframe_with_derived.dcm')
DATA_FILE_CT = pjoin(get_nibabel_data(), 'nitest-dicom', 'siemens_ct_header_csa.dcm')
DATA_FILE_SIEMENS_TRACE = pjoin(
get_nibabel_data(),
'dcm_qa_xa30',
'In/20_DWI_dir80_AP/0001_1.3.12.2.1107.5.2.43.67093.2022071112140611403312307.dcm',
)

# This affine from our converted image was shown to match our image spatially
# with an image from SPM DICOM conversion. We checked the matching with SPM
Expand Down Expand Up @@ -656,6 +661,13 @@ def test_data_derived_shape(self):
with pytest.warns(UserWarning, match='Derived images found and removed'):
assert dw.image_shape == (96, 96, 60, 33)

@dicom_test
@needs_nibabel_data('dcm_qa_xa30')
def test_data_trace(self):
# Test that a standalone trace volume is found and not dropped
dw = didw.wrapper_from_file(DATA_FILE_SIEMENS_TRACE)
assert dw.image_shape == (72, 72, 39, 1)

@dicom_test
@needs_nibabel_data('nitest-dicom')
def test_data_unreadable_private_headers(self):
Expand Down
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