Siemens B1 map with dual TR

[ghammad]

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

dcm2niix -f %p_%t_%s -i y -o dcm2niix/ ima/
grep RepetitionTime dcm2niix/kp_afib1_v1g_4mm_PA_20250217162937_2_e*.json
>> dcm2niix/kp_afib1_v1g_4mm_PA_20250217162937_2_e1.json:	"RepetitionTime": 0.025,
>> dcm2niix/kp_afib1_v1g_4mm_PA_20250217162937_2_e2.json:	"RepetitionTime": 0.025,

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:

grep RepetitionTime spm_convert/s00000000000000000000-0002-00001-0000*.json
>> spm_convert/s00000000000000000000-0002-00001-000048-01.json:			"RepetitionTime": 25,
>> spm_convert/s00000000000000000000-0002-00001-000096-02.json:			"RepetitionTime": 25,

However, the headers do contain some additional metadata, such as "alTR" that does contain the list of TR (although in a different unit):

grep alTR spm_convert/s00000000000000000000-0002-00001-0000*.json 
>> spm_convert/s00000000000000000000-0002-00001-000048-01.json:			"alTR": [25000,125000],
>> spm_convert/s00000000000000000000-0002-00001-000096-02.json:			"alTR": [25000,125000],

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

Chris Rorden's dcm2niiX version v1.0.20241231  (JP2:OpenJPEG) (JP-LS:CharLS) GCC9.4.0 x86-64 (64-bit Linux)
Found 199 DICOM file(s)
Ignoring localizer (sequence '*qfl2d1') of series 1 ima/AFI_TEST.MR.PROTOCOLS_STUDIES.0001.0001.2025.02.18.10.41.43.88002.83659872.IMA
Ignoring localizer (sequence '*qfl2d1') of series 1 ima/AFI_TEST.MR.PROTOCOLS_STUDIES.0001.0002.2025.02.18.10.41.43.88002.83659928.IMA
Ignoring localizer (sequence '*qfl2d1') of series 1 ima/AFI_TEST.MR.PROTOCOLS_STUDIES.0001.0003.2025.02.18.10.41.43.88002.83659910.IMA
Slices not stacked: echo varies (TE 3.3, 3.3; echo 1, 2). Use 'merge 2D slices' option to force stacking
::autoBids:Siemens CSAseqFname:'%CustomerSeq%\kp_afib1_v1g' pulseSeq:'' seqName:'kpafi1g3d2'
Convert 48 DICOM as dcm2niix/00000000000000000000_kp_afib1_v1g_4mm_PA_trueform_20250217162937_3_e1 (56x64x48x1)
::autoBids:Siemens CSAseqFname:'%CustomerSeq%\kp_afib1_v1g' pulseSeq:'' seqName:'kpafi1g3d2'
Convert 48 DICOM as dcm2niix/00000000000000000000_kp_afib1_v1g_4mm_PA_trueform_20250217162937_3_e2 (56x64x48x1)
::autoBids:Siemens CSAseqFname:'%CustomerSeq%\kp_afib1_v1g' pulseSeq:'' seqName:'kpafi1g3d2'
Convert 48 DICOM as dcm2niix/00000000000000000000_kp_afib1_v1g_4mm_PA_20250217162937_2_e2 (56x64x48x1)
::autoBids:Siemens CSAseqFname:'%CustomerSeq%\kp_afib1_v1g' pulseSeq:'' seqName:'kpafi1g3d2'
Convert 48 DICOM as dcm2niix/00000000000000000000_kp_afib1_v1g_4mm_PA_20250217162937_2_e1 (56x64x48x1)
Conversion required 0.394387 seconds (0.242579 for core code).

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 development branch, commit c26502a6f2820ed7cc122ab8803579ffd5b88512 (2025/01/20)

Troubleshooting

We also tried with the latest release (version 11-December-2024) before using the source code in the development branch. The outcome was identical.

Thank you for your help.

[ghammad]

We just sent you a link to our institutional file storage system (Dox, Univeristy of Liège) where you can find AFI B1 test data made with a phantom.

Best regards,

Grégory