Summary of what happened:
Hello,
I am preprocessing NAPLS3 dataset, which has older gradient echo fieldmaps from GE scanners.
The resulting phase images have bands in them that may be related to improper unwrapping. This is the case for both the phase images output from dcm2niix and for phase images generated by using the real and imaginary images output from dcm2niix (fslcomplex -complex followed by fslcomplex -realphase). I aim to generate a phasediff image for downstream qunex starting with hcp_prefreesurfer.
Example of a phase images is attached below from one subject in site 4. Any suggestions on how to fix this data and ultimately generate unwrapped phasediff images that are suitable for qunex hcp_prefreesurfer?
Command used (and if a helper script was used, a link to the helper script or the command generated):
using code from Wengler-Lab · GitHub
PASTE CODE HERE
Version:
dcm2niix/1.0.20250506
Environment (Docker, Singularity / Apptainer, custom installation):
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE
