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

Output "sub-01" (MultipartID auto+concat+0 [inferred]): 3 series
  Distortion group sub-01_dir-AP_run-1 (PE j-, TRT 0.05s):
    - sub-01_dir-AP_run-1_dwi.nii.gz
    corrected by: pepolar01 [curated]
  Distortion group sub-01_dir-AP_run-2 (PE j-, TRT 0.05s):
    - sub-01_dir-AP_run-2_dwi.nii.gz
    corrected by: auto+synb0 [inferred]
  Distortion group sub-01_dir-PA_run-1 (PE j, TRT 0.05s):
    - sub-01_dir-PA_run-1_dwi.nii.gz
    corrected by: pepolar01 [curated]

Fieldmap estimations:
  auto+synb0 [inferred]: SyNb0 synthetic b=0
    - sub-01_T1w.nii.gz
  pepolar01 [curated]: PEPOLAR (reverse phase-encoding)
    - sub-01_dir-AP_run-1_dwi.nii.gz
    - sub-01_dir-PA_run-1_dwi.nii.gz
    phase encoding axes: j (bidirectional)

Notes:
  WARNING [reverse-pe-not-inferred]: sub-01_dir-AP_run-2_dwi.nii.gz: this subject has fieldmaps linked by B0FieldIdentifier/B0FieldSource or IntendedFor, so QSIPrep does not infer reverse phase-encoding pairings for the remaining series; only a fieldmap-less correction (--sdc-anat-reference) reaches them. Add B0FieldIdentifier/B0FieldSource to pair them.

Processing preview: eddy + TOPUP (--hmc-method eddy --sdc-method topup)
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Output "sub-01" (3 series):
  1. Each series is denoised on its own. The 3 series span 2 correction units; each unit is concatenated and corrected in its own pipeline.
  2. Correction unit 'sub-01_dir-AP_run-2' (sub-01_dir-AP_run-2_dwi.nii.gz):
  3. SyNb0 synthesizes an undistorted b=0 image from the T1w (sub-01_T1w.nii.gz).
  4. TOPUP estimates the susceptibility field from the acquired b=0 images plus the synthetic b=0, which enters as a zero-readout-time volume (an extra row in the acquisition-parameters file).
  5. eddy corrects head motion, eddy currents, and susceptibility distortion in one model, using the TOPUP field.
  6. Correction unit 'sub-01_run-1' (sub-01_dir-AP_run-1_dwi.nii.gz, sub-01_dir-PA_run-1_dwi.nii.gz):
  7. TOPUP estimates the susceptibility field from b=0 images spanning 2 distortion groups (2 rows in the acquisition-parameters file).
  8. 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.
  9. The corrected results of the 2 units are resampled onto one grid and concatenated into one output file.

Processing preview: TORTOISE + DRBUDDI (--hmc-method tortoise --sdc-method drbuddi)
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Output "sub-01" (3 series):
  1. Each series is denoised on its own. The 3 series span 2 correction units; each unit is concatenated and corrected in its own pipeline.
  2. Correction unit 'sub-01_dir-AP_run-2' (sub-01_dir-AP_run-2_dwi.nii.gz):
  3. TORTOISE DIFFPREP corrects head motion and eddy currents.
  4. SyNb0 synthesizes an undistorted b=0 image from the T1w (sub-01_T1w.nii.gz) and the DIFFPREP-corrected b=0; TOPUP pairs the two (the synthetic b=0 as a zero-readout-time volume), and the resulting field is applied to unwarp the DIFFPREP output.
  5. Correction unit 'sub-01_run-1' (sub-01_dir-AP_run-1_dwi.nii.gz, sub-01_dir-PA_run-1_dwi.nii.gz):
  6. TORTOISE DIFFPREP corrects head motion and eddy currents separately for each distortion group (sub-01_dir-AP_run-1, sub-01_dir-PA_run-1).
  7. DRBUDDI estimates distortion along the j axis from the blip-up (sub-01_dir-PA_run-1) and blip-down (sub-01_dir-AP_run-1) data and applies the correction to every volume.
     DRBUDDI additionally uses the T2w image (sub-01_T2w.nii.gz) as a structural registration target (multimodal correction).
  8. The corrected results of the 2 units are resampled onto one grid and concatenated into one output file.

Processing preview: eddy + TOPUP→DRBUDDI (--hmc-method eddy --sdc-method topup+drbuddi)
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Output "sub-01" (3 series):
  1. Each series is denoised on its own. The 3 series span 2 correction units; each unit is concatenated and corrected in its own pipeline.
  2. Correction unit 'sub-01_dir-AP_run-2' (sub-01_dir-AP_run-2_dwi.nii.gz):
  3. SyNb0 synthesizes an undistorted b=0 image from the T1w (sub-01_T1w.nii.gz); TOPUP treats it as a zero-readout-time volume, and eddy corrects head motion, eddy currents, and susceptibility distortion in one model using the resulting field. With no reverse phase-encoded dMRI series the DRBUDDI second stage does not run.
  4. Correction unit 'sub-01_run-1' (sub-01_dir-AP_run-1_dwi.nii.gz, sub-01_dir-PA_run-1_dwi.nii.gz):
  5. TOPUP estimates an initial susceptibility field from the b=0 images (as in the FSL path).
  6. eddy corrects head motion and eddy currents using the TOPUP field.
  7. DRBUDDI re-estimates distortion along the j axis from the eddy-corrected blip-up/blip-down dMRI series, refining the TOPUP correction.
     DRBUDDI additionally uses the T2w image (sub-01_T2w.nii.gz) as a structural registration target (multimodal correction).
  8. The corrected results of the 2 units are resampled onto one grid and concatenated into one output file.

Processing preview: SHORELine + DRBUDDI (--hmc-method shoreline --sdc-method drbuddi)
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Output "sub-01" (3 series):
  1. Each series is denoised on its own. The 3 series span 2 correction units; each unit is concatenated and corrected in its own pipeline.
  2. Correction unit 'sub-01_dir-AP_run-2' (sub-01_dir-AP_run-2_dwi.nii.gz):
  3. SHORELine iteratively corrects head motion by registering each volume to a 3dSHORE signal-model prediction (eddy currents are not corrected).
  4. SyNb0 synthesizes an undistorted b=0 image from the T1w (sub-01_T1w.nii.gz) and the SHORELine-corrected b=0; TOPUP pairs the two (the synthetic b=0 as a zero-readout-time volume), and the resulting field is applied to unwarp the corrected series.
  5. Correction unit 'sub-01_run-1' (sub-01_dir-AP_run-1_dwi.nii.gz, sub-01_dir-PA_run-1_dwi.nii.gz):
  6. SHORELine iteratively corrects head motion by registering each volume to a 3dSHORE signal-model prediction (eddy currents are not corrected).
  7. DRBUDDI estimates distortion along the j axis from the blip-up (sub-01_dir-PA_run-1) and blip-down (sub-01_dir-AP_run-1) data and applies the correction to every volume.
     DRBUDDI additionally uses the T2w image (sub-01_T2w.nii.gz) as a structural registration target (multimodal correction).
  8. The corrected results of the 2 units are resampled onto one grid and concatenated into one output file.
