DWI grouping for sub-01
=======================

Output "sub-01_ses-1_dir-AP" (MultipartID auto+concat+ses-1+0 [inferred]): 1 series
  Distortion group sub-01_ses-1_dir-AP (PE j-, TRT 0.05s):
    - sub-01_ses-1_dir-AP_dwi.nii.gz
    corrected by: shared_field [curated]

Output "sub-01_ses-2_dir-AP" (MultipartID auto+concat+ses-2+1 [inferred]): 1 series
  Distortion group sub-01_ses-2_dir-AP (PE j-, TRT 0.05s):
    - sub-01_ses-2_dir-AP_dwi.nii.gz
    corrected by: shared_field [curated]

Fieldmap estimations:
  shared_field [curated]: PEPOLAR (reverse phase-encoding)
    - sub-01_dir-AP_epi.nii.gz
    - sub-01_dir-PA_epi.nii.gz
    phase encoding axes: j (bidirectional)

Notes:
  WARNING [cross-session-fieldmap-application]: Fieldmap estimation 'shared_field' corrects DWI series in multiple sessions (ses-1, ses-2). The linkage is explicit and will be honored, but sessions are usually re-shimmed - verify that one fieldmap really applies to all of them.
  WARNING [estimation-spans-outputs]: Fieldmap estimation 'shared_field' corrects DWI series in 2 different correction units; it will be estimated once per unit.

Processing preview: eddy + TOPUP (--hmc-method eddy --sdc-method topup)
-----------------------------------------------------------------------

Output "sub-01_ses-1_dir-AP" (1 single series):
  1. The series is denoised.
  2. TOPUP estimates the susceptibility field from b=0 images spanning 2 distortion groups (2 rows in the acquisition-parameters file).
     Extra b=0 images from fmap/: sub-01_dir-AP_epi.nii.gz, sub-01_dir-PA_epi.nii.gz.
  3. eddy corrects head motion, eddy currents, and susceptibility distortion in one model, using the TOPUP field. Every volume is assigned to its distortion group in the eddy index file.
  4. The corrected series is written as one output file.

Output "sub-01_ses-2_dir-AP" (1 single series):
  1. The series is denoised.
  2. TOPUP estimates the susceptibility field from b=0 images spanning 2 distortion groups (2 rows in the acquisition-parameters file).
     Extra b=0 images from fmap/: sub-01_dir-AP_epi.nii.gz, sub-01_dir-PA_epi.nii.gz.
  3. eddy corrects head motion, eddy currents, and susceptibility distortion in one model, using the TOPUP field. Every volume is assigned to its distortion group in the eddy index file.
  4. The corrected series is written as one output file.

Processing preview: TORTOISE + DRBUDDI (--hmc-method tortoise --sdc-method drbuddi)
-----------------------------------------------------------------------------------

Output "sub-01_ses-1_dir-AP" (1 single series):
  1. The series is denoised.
  2. TORTOISE DIFFPREP corrects head motion and eddy currents.
  3. DRBUDDI estimates distortion along the j axis from the blip-up (borrowed series) and blip-down (sub-01_ses-1_dir-AP) data and applies the correction to every volume.
  4. The corrected series is written as one output file.

Output "sub-01_ses-2_dir-AP" (1 single series):
  1. The series is denoised.
  2. TORTOISE DIFFPREP corrects head motion and eddy currents.
  3. DRBUDDI estimates distortion along the j axis from the blip-up (borrowed series) and blip-down (sub-01_ses-2_dir-AP) data and applies the correction to every volume.
  4. The corrected series is written as one output file.

Processing preview: eddy + TOPUP→DRBUDDI (--hmc-method eddy --sdc-method topup+drbuddi)
---------------------------------------------------------------------------------------

Output "sub-01_ses-1_dir-AP" (1 single series):
  1. The series is denoised.
  2. TOPUP estimates an initial susceptibility field from the b=0 images (as in the FSL path).
  3. eddy corrects head motion and eddy currents using the TOPUP field.
  4. There is no reverse phase-encoded dMRI series for DRBUDDI to refine with, and no T2w or synthetic b=0 for a T2Wreg stage: correction is single-stage (TOPUP + eddy).
  5. The corrected series is written as one output file.
  !! WARNING [drbuddi-refinement-not-useful]: Estimation 'shared_field' has no reverse phase-encoded dMRI series: a DRBUDDI second stage would reuse the same b=0 images TOPUP already consumed and is probably not useful. No T2w or SyNb0 synthetic b=0 is available for a T2Wreg second stage either, so 'sub-01_ses-1_dir-AP' gets single-stage (TOPUP+eddy) correction.

Output "sub-01_ses-2_dir-AP" (1 single series):
  1. The series is denoised.
  2. TOPUP estimates an initial susceptibility field from the b=0 images (as in the FSL path).
  3. eddy corrects head motion and eddy currents using the TOPUP field.
  4. There is no reverse phase-encoded dMRI series for DRBUDDI to refine with, and no T2w or synthetic b=0 for a T2Wreg stage: correction is single-stage (TOPUP + eddy).
  5. The corrected series is written as one output file.
  !! WARNING [drbuddi-refinement-not-useful]: Estimation 'shared_field' has no reverse phase-encoded dMRI series: a DRBUDDI second stage would reuse the same b=0 images TOPUP already consumed and is probably not useful. No T2w or SyNb0 synthetic b=0 is available for a T2Wreg second stage either, so 'sub-01_ses-2_dir-AP' gets single-stage (TOPUP+eddy) correction.

Processing preview: SHORELine + DRBUDDI (--hmc-method shoreline --sdc-method drbuddi)
-------------------------------------------------------------------------------------

Output "sub-01_ses-1_dir-AP" (1 single series):
  1. The series is denoised.
  2. SHORELine iteratively corrects head motion by registering each volume to a 3dSHORE signal-model prediction (eddy currents are not corrected).
  3. DRBUDDI estimates distortion along the j axis from the blip-up (borrowed series) and blip-down (sub-01_ses-1_dir-AP) data and applies the correction to every volume.
  4. The corrected series is written as one output file.

Output "sub-01_ses-2_dir-AP" (1 single series):
  1. The series is denoised.
  2. SHORELine iteratively corrects head motion by registering each volume to a 3dSHORE signal-model prediction (eddy currents are not corrected).
  3. DRBUDDI estimates distortion along the j axis from the blip-up (borrowed series) and blip-down (sub-01_ses-2_dir-AP) data and applies the correction to every volume.
  4. The corrected series is written as one output file.
