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

Output "sub-01" (MultipartID auto+concat+0 [inferred]): 4 series
  Distortion group sub-01_acq-fast_dir-AP (PE j-, TRT 0.05s):
    - sub-01_acq-fast_dir-AP_dwi.nii.gz [shelled: b=1000/2000]
    corrected by: multiread [curated]
  Distortion group sub-01_acq-fast_dir-PA (PE j, TRT 0.05s):
    - sub-01_acq-fast_dir-PA_dwi.nii.gz [shelled: b=1000/2000]
    corrected by: multiread [curated]
  Distortion group sub-01_acq-slow_dir-AP (PE j-, TRT 0.08s):
    - sub-01_acq-slow_dir-AP_dwi.nii.gz [shelled: b=1000/2000]
    corrected by: multiread [curated]
  Distortion group sub-01_acq-slow_dir-PA (PE j, TRT 0.08s):
    - sub-01_acq-slow_dir-PA_dwi.nii.gz [shelled: b=1000/2000]
    corrected by: multiread [curated]

Fieldmap estimations:
  multiread [curated]: PEPOLAR (reverse phase-encoding)
    - sub-01_acq-fast_dir-AP_dwi.nii.gz
    - sub-01_acq-fast_dir-PA_dwi.nii.gz
    - sub-01_acq-slow_dir-AP_dwi.nii.gz
    - sub-01_acq-slow_dir-PA_dwi.nii.gz
    phase encoding axes: j (bidirectional)

Processing preview: eddy + TOPUP (--hmc-method eddy --sdc-method topup)
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Output "sub-01" (4 series):
  1. Each series is denoised on its own, then all 4 series are concatenated. (--denoise-after-combining reverses this order.)
  2. TOPUP estimates the susceptibility field from b=0 images spanning 4 distortion groups (4 rows in the acquisition-parameters file).
  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)
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Output "sub-01" (4 series):
  1. Each series is denoised on its own, then all 4 series are concatenated. (--denoise-after-combining reverses this order.)
  2. TORTOISE DIFFPREP corrects head motion and eddy currents separately for each distortion group (sub-01_acq-fast_dir-AP, sub-01_acq-fast_dir-PA, sub-01_acq-slow_dir-AP, sub-01_acq-slow_dir-PA).
     Estimation forms 2 blip pairs (axis j, TRT 0.05s; axis j, TRT 0.08s); each is corrected in its own DIFFPREP+DRBUDDI pipeline and the corrected results are combined.
  3. DRBUDDI estimates distortion along the j axis (TRT 0.05s) from the blip-up (sub-01_acq-fast_dir-PA) and blip-down (sub-01_acq-fast_dir-AP) data and applies the correction to every volume.
  4. DRBUDDI estimates distortion along the j axis (TRT 0.08s) from the blip-up (sub-01_acq-slow_dir-PA) and blip-down (sub-01_acq-slow_dir-AP) data and applies the correction to every volume.
  5. The corrected series is written as one output file.

Processing preview: eddy + TOPUP→DRBUDDI (--hmc-method eddy --sdc-method topup+drbuddi)
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Output "sub-01" (4 series):
  1. Each series is denoised on its own, then all 4 series are concatenated. (--denoise-after-combining reverses this order.)
  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. The estimation spans 2 blip groups (axis j, TRT 0.05s; axis j, TRT 0.08s); TOPUP+eddy corrects them together, but the single-pass DRBUDDI refinement covers one matched pair, so no DRBUDDI refinement is applied.
  5. The corrected series is written as one output file.
  !! WARNING [drbuddi-refinement-multigroup]: Estimation 'multiread' spans 2 blip groups (axis j, TRT 0.05s; axis j, TRT 0.08s). TOPUP+eddy corrects them together, but the DRBUDDI refinement handles one matched pair at a time, so 'sub-01' gets single-stage TOPUP+eddy correction (no DRBUDDI refinement).

Processing preview: SHORELine + DRBUDDI (--hmc-method shoreline --sdc-method drbuddi)
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Output "sub-01" (4 series):
  1. Each series is denoised on its own, then all 4 series are concatenated. (--denoise-after-combining reverses this order.)
  2. SHORELine iteratively corrects head motion by registering each volume to a 3dSHORE signal-model prediction (eddy currents are not corrected).
     Estimation forms 2 blip pairs (axis j, TRT 0.05s; axis j, TRT 0.08s); each is corrected in its own SHORELine+DRBUDDI pipeline and the corrected results are combined.
  3. DRBUDDI estimates distortion along the j axis (TRT 0.05s) from the blip-up (sub-01_acq-fast_dir-PA) and blip-down (sub-01_acq-fast_dir-AP) data and applies the correction to every volume.
  4. DRBUDDI estimates distortion along the j axis (TRT 0.08s) from the blip-up (sub-01_acq-slow_dir-PA) and blip-down (sub-01_acq-slow_dir-AP) data and applies the correction to every volume.
  5. The corrected series is written as one output file.
