Two field map pairs in a single session (error: "Sophisticated PEPOLAR schemes are unsupported")

[yanbin-niu]

Hello,

We are using nibabies for our infant MRI preprocessing. In our project, each session includes two pairs of field maps — one acquired at the beginning and another at the end of the scan. For example,

fmap:

sub-12018_ses-newborn_acq-rest_dir-AP_run-01_epi.nii.gz,
sub-12018_ses-newborn_acq-rest_dir-AP_run-02_epi.nii.gz,
sub-12018_ses-newborn_acq-rest_dir-PA_run-01_epi.nii.gz,
sub-12018_ses-newborn_acq-rest_dir-PA_run-02_epi.nii.gz
and we set up the "IntendedFor" for all func runs.

When we run nibabies on these data, the pipeline fails and reports the following error message:

Traceback (most recent call last):
File "/opt/conda/envs/nibabies/bin/nibabies", line 8, in sys.exit(main()) ^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/run.py", line 62, in main retval = build_workflow(config_file) ^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/workflow.py", line 76, in build_workflow retval['workflow'] = init_nibabies_wf(config.execution.unique_labels) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/workflows/base.py", line 147, in init_nibabies_wf single_subject_wf = init_single_subject_wf( ^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/workflows/base.py", line 628, in init_single_subject_wf
raise NotImplementedError('Sophisticated PEPOLAR schemes are unsupported.')
NotImplementedError: Sophisticated PEPOLAR schemes are unsupported.

It seems that nibabies currently doesn’t support multiple field map pairs within a single session. I also checked the latest release notes and documentation but didn’t see updates addressing this issue. Am I handle this correctly or is there currently any workaround to handle multiple field map pairs (e.g., by combining two together)?

Thank you for your help!

[mgxd]

Hi, we have not implemented that correction scheme - generally a single opposing pair of EPIs does a decent job. Just curious, how have you previously processed this data (if you have)?

[yanbin-niu]

Thanks, @mgxd , for the quick reply! To be honest, this is our first project with two pairs of PA/AP field maps in a single session. I think we can drop one to make it work. But I am curious -- we actually borrowed the exam card from HBCD. So any chance you know how HBCD handles having two field map pairs?

[mgxd]

It's common to acquire a new run of opposing EPIs prior to each functional scan, so my guess would be that *run-01_epis would pertain to *run-01_bold, and *run-02_epi would be used for *run-02_bold - but I would check with the scanner protocol to be sure.

[yanbin-niu]

Thanks @mgxd !