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

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

Output "sub-01_dir-AP_run-2" (MultipartID auto+concat+1 [inferred]): 1 series
  Distortion group sub-01_dir-AP_run-2 (PE j-, TRT 0.05s):
    - sub-01_dir-AP_run-2_dwi.nii.gz
    corrected by: nothing (no fieldmap found)

Output "sub-01_dir-PA_run-2" (MultipartID auto+concat+2 [inferred]): 1 series
  Distortion group sub-01_dir-PA_run-2 (PE j, TRT 0.05s):
    - sub-01_dir-PA_run-2_dwi.nii.gz
    corrected by: nothing (no fieldmap found)

Fieldmap estimations:
  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, sub-01_dir-PA_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_run-1" (2 series):
  1. Each series is denoised on its own, then all 2 series are concatenated.
  2. TOPUP estimates the susceptibility field from b=0 images spanning 2 distortion groups (2 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.

Output "sub-01_dir-AP_run-2" (1 single series):
  1. The series is denoised.
  2. eddy corrects head motion and eddy currents. No fieldmap is available and fieldmap-less SDC is disabled (--sdc-anat-reference none): susceptibility distortion is NOT corrected.
  3. The corrected series is written as one output file.
  !! WARNING [no-sdc]: Output 'sub-01_dir-AP_run-2' has no fieldmap and no fieldmap-less correction was requested: no susceptibility distortion correction will be performed. Pass --sdc-anat-reference synb0 to correct it with a synthetic b=0 from the T1w (SynB0 + TOPUP).

Output "sub-01_dir-PA_run-2" (1 single series):
  1. The series is denoised.
  2. eddy corrects head motion and eddy currents. No fieldmap is available and fieldmap-less SDC is disabled (--sdc-anat-reference none): susceptibility distortion is NOT corrected.
  3. The corrected series is written as one output file.
  !! WARNING [no-sdc]: Output 'sub-01_dir-PA_run-2' has no fieldmap and no fieldmap-less correction was requested: no susceptibility distortion correction will be performed. Pass --sdc-anat-reference synb0 to correct it with a synthetic b=0 from the T1w (SynB0 + TOPUP).

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

Output "sub-01_run-1" (2 series):
  1. Each series is denoised on its own, then all 2 series are concatenated.
  2. 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).
  3. 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.
  4. The corrected series is written as one output file.

Output "sub-01_dir-AP_run-2" (1 single series):
  1. The series is denoised.
  2. TORTOISE DIFFPREP corrects head motion and eddy currents.
  3. No fieldmap is available and fieldmap-less SDC is disabled (--sdc-anat-reference none): susceptibility distortion is NOT corrected.
  4. The corrected series is written as one output file.
  !! WARNING [no-sdc]: Output 'sub-01_dir-AP_run-2' has no fieldmap and no fieldmap-less correction was requested: no susceptibility distortion correction will be performed. Pass --sdc-anat-reference synb0 to correct it with a synthetic b=0 from the T1w (SynB0 + TOPUP).

Output "sub-01_dir-PA_run-2" (1 single series):
  1. The series is denoised.
  2. TORTOISE DIFFPREP corrects head motion and eddy currents.
  3. No fieldmap is available and fieldmap-less SDC is disabled (--sdc-anat-reference none): susceptibility distortion is NOT corrected.
  4. The corrected series is written as one output file.
  !! WARNING [no-sdc]: Output 'sub-01_dir-PA_run-2' has no fieldmap and no fieldmap-less correction was requested: no susceptibility distortion correction will be performed. Pass --sdc-anat-reference synb0 to correct it with a synthetic b=0 from the T1w (SynB0 + TOPUP).

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

Output "sub-01_run-1" (2 series):
  1. Each series is denoised on its own, then all 2 series are concatenated.
  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. DRBUDDI re-estimates distortion along the j axis from the eddy-corrected blip-up/blip-down dMRI series, refining the TOPUP correction.
  5. The corrected series is written as one output file.

Output "sub-01_dir-AP_run-2" (1 single series):
  1. The series is denoised.
  2. No fieldmap is available and fieldmap-less SDC is disabled (--sdc-anat-reference none): susceptibility distortion is NOT corrected.
  3. The corrected series is written as one output file.
  !! WARNING [no-sdc]: Output 'sub-01_dir-AP_run-2' has no fieldmap and no fieldmap-less correction was requested: no susceptibility distortion correction will be performed. Pass --sdc-anat-reference synb0 to correct it with a synthetic b=0 from the T1w (SynB0 + TOPUP).

Output "sub-01_dir-PA_run-2" (1 single series):
  1. The series is denoised.
  2. No fieldmap is available and fieldmap-less SDC is disabled (--sdc-anat-reference none): susceptibility distortion is NOT corrected.
  3. The corrected series is written as one output file.
  !! WARNING [no-sdc]: Output 'sub-01_dir-PA_run-2' has no fieldmap and no fieldmap-less correction was requested: no susceptibility distortion correction will be performed. Pass --sdc-anat-reference synb0 to correct it with a synthetic b=0 from the T1w (SynB0 + TOPUP).

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

Output "sub-01_run-1" (2 series):
  1. Each series is denoised on its own, then all 2 series are concatenated.
  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 (sub-01_dir-PA_run-1) and blip-down (sub-01_dir-AP_run-1) data and applies the correction to every volume.
  4. The corrected series is written as one output file.

Output "sub-01_dir-AP_run-2" (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. No fieldmap is available and fieldmap-less SDC is disabled (--sdc-anat-reference none): susceptibility distortion is NOT corrected.
  4. The corrected series is written as one output file.
  !! WARNING [no-sdc]: Output 'sub-01_dir-AP_run-2' has no fieldmap and no fieldmap-less correction was requested: no susceptibility distortion correction will be performed. Pass --sdc-anat-reference synb0 to correct it with a synthetic b=0 from the T1w (SynB0 + TOPUP).

Output "sub-01_dir-PA_run-2" (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. No fieldmap is available and fieldmap-less SDC is disabled (--sdc-anat-reference none): susceptibility distortion is NOT corrected.
  4. The corrected series is written as one output file.
  !! WARNING [no-sdc]: Output 'sub-01_dir-PA_run-2' has no fieldmap and no fieldmap-less correction was requested: no susceptibility distortion correction will be performed. Pass --sdc-anat-reference synb0 to correct it with a synthetic b=0 from the T1w (SynB0 + TOPUP).
