Siemens XA60 conversion of diffusion data

[jonbpanda]

Describe the bug

Not sure this is a bug! Acquired multi-shell diffusion data according to the HCP-D/A protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6484842/)

Note that the data were acquired with the Siemens product multi-band sequence (not the CMRR version), so every slice for each direction/b-value combination is saved as a separate image (rather than mosaic'ed). There were 92 slices per volume, which relates to the Warning below

However, dcm2niix took absolutely ages (>1 hour) to parse the DICOM folder on a relatively speedy machine.

To reproduce

Steps to reproduce the behavior:

1. Download the DICOM data (will send via separate email)
2. Convert using command: dcm2niix -f series%s_%p -z y -o ./Converted ./DICOM
3. See slow behaviour
4. 1000s of warnings (as described on neurostars):
   E.g. Warning: Series 30074 includes partial volume (issue 742): 1 slices acquired but ICE dims {0021, 118e} specifies 92

Expected behavior

Would like to think that dcm2niix could resolve this problem of non-mosaic'ed data and reconstitute the desired volumes - even better if it could munge it into a 4D file and generate the associated bvec and bval files.

Output log

N/A

Version

Please report the complete version string:

dcm2niiX version v1.0.20240202 GCC12.3.0 x86-64 (64-bit Linux)

Troubleshooting

Please try the following steps to resolve your issue:

Latest stable release AFAIK

git clone --branch development https://github.com/rordenlab/dcm2niix.git
cd dcm2niix/console
make
./dcm2niix ....

Haven't had a chance to try this yet. Will try when I have a moment.

[mharms]

FYI: If you export as "Enhanced" DICOM from XA, you'll get 1 DICOM per frame/volume, which is much easier to work with.