Missing PhaseEncodingDirection from ASL JSON

[echumin]

Describe the bug
I am running dcm2niix through dcm2bids (3.2.0). I have two asl series in opposite phase encoding "j" and "j-" and I was using the "PhaseEncodingDirection" json tag to bids pair the data.

After upgrading dcm2niix to 2024.12.11 (from 2024.02.02) the "PhaseEncodingDirection" tag is no longer in the ASL json files. I get the same when I revert to the 2024.12.08 version.

dcm2niix command example:
dcm2niix -b y -ba n -z y -f %3s_%f_%p_%t -o asl/ sourcedata/DRTS0072/10-tgse_pcasl_5delay_3.5iso_AP

Version
Chris Rorden's dcm2niiX version v1.0.20241211 GCC9.3.0 x86-64 (64-bit Linux)
v1.0.20241211

[neurolabusc]

@echumin can you provide a bit more feedback - perhaps insert the text from the json file for the image in question. Given the file name, I assme that this data if from a Siemens scanner, similar to the TGSE ASL dataset here, but it is unclear if your system is V* or XA*. Also, it is unclear if this is a 2D or a 3D acquisition. I am going to go out on a limb here and suggest that your image is a "MRAcquisitionType": "3D". While 2D EPI data wraps phase in one direction, the 3D acquisitions wrap in two directions. I am unsure how to decode the second wrapping direction (e.g. is it always in the slice direction), nor is it clear that their are tools to undistort these images using this information. If your data is Siemens 3D, I think we need some guidance on the proper BIDS nomenclature (and perhaps help from the Siemens Research Collaboration Manager associated with your center).

[echumin]

You are correct, it it a Siemens Prisma, 3D multidelay PCASL acquistion.

Here are two json files from the same scan series, one generated by the Feb2024 dcm2niix release and another by the latest release (20241211).
010_10-tgse_pcasl_5delay_3.5iso_AP_tgse_pcasl_5delay_3.5iso_AP_20241002144838_v20240202.json
010_10-tgse_pcasl_5delay_3.5iso_AP_tgse_pcasl_5delay_3.5iso_AP_20241002144838_v20241211.json

I can use the sequence name to get the direction information for the bids dir-, but I thought it odd that the 20240202 dcm2niix puts phase encoding in the json, while the latest 20241211 does not do it.