Siemens B1 map with dual TR #918
Comments
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We just sent you a link to our institutional file storage system (Dox, University of Liège) where you can find AFI B1 test data made with a phantom. Best regards, Grégory |
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The link to the shared data might expire at some point. May I ask you to confirm that you received the test data? Thank you. Best regards, Grégory |
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dcm2niix is correctly following the recipe of the DICOM images. You can see that yourself by running this Python script. The series claims to have two echoes, but only a single TR. All images in the series claim identical TR and TE times. python dcm_values.py ./issue918
2 1 1 2.13 25
2 2 1 2.13 25
2 3 1 2.13 25
2 4 1 2.13 25
2 5 1 2.13 25
2 6 1 2.13 25
2 7 1 2.13 25
2 8 1 2.13 25
2 9 1 2.13 25
...
2 47 1 2.13 25
2 48 1 2.13 25
2 49 2 2.13 25
2 50 2 2.13 25
...
2 94 2 2.13 25
2 95 2 2.13 25
2 96 2 2.13 25dcm2niix and dicm2nii have the same interpretation (albeit dicm2nii concatenates each echo in a single 4D file, while dcm2niix follows the BIDS specification to save each echo as a separate file). You can merge 3D NIfTI files as a 4D file with import os
import sys
import pydicom
def extract_dicom_info(filepath):
try:
ds = pydicom.dcmread(filepath, stop_before_pixels=True)
series_number = getattr(ds, 'SeriesNumber', 0)
instance_number = getattr(ds, 'InstanceNumber', 0)
echo_number = getattr(ds, 'EchoNumbers', 0)
echo_time = getattr(ds, 'EchoTime', 0)
repetition_time = getattr(ds, 'RepetitionTime', 0)
return series_number, instance_number, echo_number, echo_time, repetition_time
except Exception as e:
print(f"Warning: Failed to read {filepath}: {e}", file=sys.stderr)
return None
def main():
if len(sys.argv) != 2:
print(f"Usage: {sys.argv[0]} <folder>")
sys.exit(1)
folder = sys.argv[1]
if not os.path.isdir(folder):
print(f"Error: '{folder}' is not a valid directory.")
sys.exit(1)
dicom_files = []
for filename in os.listdir(folder):
if filename.lower().endswith('.dcm'):
filepath = os.path.join(folder, filename)
info = extract_dicom_info(filepath)
if info:
dicom_files.append(info)
# Sort by series number, then instance number
dicom_files.sort(key=lambda x: (x[0], x[1]))
# Output header (optional, remove if not needed)
# print("SeriesNumber\tInstanceNumber\tEchoNumber\tEchoTime\tRepetitionTime")
for series_number, instance_number, echo_number, echo_time, repetition_time in dicom_files:
print(f"{series_number}\t{instance_number}\t{echo_number}\t{echo_time}\t{repetition_time}")
if __name__ == "__main__":
main() |
Describe the bug
Similarly to #743 , our B1 mapping on a Siemens Terra uses a dual TR AFI protocol. When converting the DICOM images with dcm2niix, we end up with 2 images with "_e1.nii" and "_e2.nii" as suffixes. So far, so good. However, when looking into the associated .json files, we noticed that the "RepetitionTime" fields are identical between the 2 resulting images.
To reproduce
Expected behavior
The field "RepetitionTime" of the second image ("_e2.nii/json") should report the second TR.
For completeness, we also ran the DICOM to Nifti conversion from SPM12.6. The reported "RepetitionTime" are also identical between the two images:
However, the headers do contain some additional metadata, such as "alTR" that does contain the list of TR (although in a different unit):
This SPM workflow is what we usually use in our lab but we would like to be able to use dcm2niix, precisely to avoid having to parse additional metadata based on the sequence type.
We fully understand the dcm2niix cannot accommodate all sequence configurations but we would grateful if you could suggest a way to extract the expected TR with dcm2niix.
Output log
Version
dcm2niiX version v1.0.20241231 (JP2:OpenJPEG) (JP-LS:CharLS) GCC9.4.0 x86-64 (64-bit Linux)This build was created with the code under the
developmentbranch, commitc26502a6f2820ed7cc122ab8803579ffd5b88512(2025/01/20)Troubleshooting
We also tried with the latest release (version 11-December-2024) before using the source code in the
developmentbranch. The outcome was identical.Thank you for your help.
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