Drop QSIPrep-specific config elements.

qsirecon/config.py

@@ -418,37 +418,19 @@ class execution(_Config):
     """Do not collect telemetry information for *QSIRecon*."""
     output_dir = None
     """Folder where derivatives will be stored."""
-    output_layout = None
-    """Layout of derivatives within output_dir."""
     # output_spaces = None
     # """List of (non)standard spaces designated (with the ``--output-spaces`` flag of
     # the command line) as spatial references for outputs."""
     reports_only = False
     """Only build the reports, based on the reportlets found in a cached working directory."""
     run_uuid = f"{strftime('%Y%m%d-%H%M%S')}_{uuid4()}"
     """Unique identifier of this particular run."""
-    skip_odf_reports = False
-    """Disable ODF recon reports."""
     participant_label = None
     """List of participant identifiers that are to be preprocessed."""
-    qsirecon_dir = None
-    """Root of QSIRecon BIDS Derivatives dataset. Depends on output_layout."""
-    qsirecon_dir = None
-    """Root of QSIRecon BIDS Derivatives dataset."""
-    recon_input = None
-    """Directory containing QSIRecon derivatives to run through recon workflows."""
     freesurfer_input = None
     """Directory containing FreeSurfer directories to use for recon workflows."""
-    recon_only = False
-    """Run only recon workflows."""
     reportlets_dir = None
     """Path where reportlets are written."""
-    run_preproc_and_recon = False
-    """Will both preproc and recon be run in a single call?"""
-    skip_anat_based_spatial_normalization = False
-    """Should we skip normalizing the anatomical data to a template?"""
-    task_id = None
-    """Select a particular task from all available in the dataset."""
     templateflow_home = _templateflow_home
     """The root folder of the TemplateFlow client."""
     work_dir = Path("work").absolute()
@@ -471,9 +453,6 @@ class execution(_Config):
         "layout",
         "log_dir",
         "output_dir",
-        "qsirecon_dir",
-        "qsirecon_dir",
-        "recon_input",
         "reportlets_dir",
         "templateflow_home",
         "work_dir",
@@ -567,83 +546,14 @@ def _process_value(value):
 class workflow(_Config):
     """Configure the particular execution graph of this workflow."""
 
-    anat_modality = None
-    """Modality to use as the anatomical reference. Images of this
-    contrast will be skull stripped and segmented for use in the
-    visual reports and reconstruction. If --infant, T2w is forced."""
-    anat_only = False
-    """Execute the anatomical postprocessing only."""
-    anatomical_template = None
-    """Keeps the :py:class:`~niworkflows.utils.spaces.SpatialReferences`
-    instance keeping standard and nonstandard spaces."""
-    b0_threshold = None
-    """Any value in the .bval file less than this will be considered a b=0 image."""
-    b0_motion_corr_to = None
-    """Perform SHORELine's initial b=0-based registration to first volume?
-    Or make a template? Either 'iterative' or 'first'"""
-    b0_to_t1w_transform = None
-    """Transformation model for intramodal registration."""
-    b1_biascorrect_stage = None
-    """The stage of processing at which to apply B1 bias correction. Either "final" (after
-    resampling), "none" (skipped entirely) or "legacy" (before concatenation)."""
-    cifti_output = None
-    """Generate HCP Grayordinates, accepts either ``'91k'`` (default) or ``'170k'``."""
-    denoise_after_combining = False
-    """Run ``dwidenoise`` after combining dwis, but before motion correction."""
-    denoise_method = None
-    """Image-based denoising method. Either "dwidenoise" (MRtrix), "patch2self" (DIPY)
-    or "none"."""
-    distortion_group_merge = None
-    """How to combine images across distortion groups (concatenate, average or none)."""
-    do_reconall = True
-    """Run FreeSurfer's surface reconstruction (ignored)."""
-    dwi_denoise_window = None
-    """Window size in voxels for image-based denoising, integer or "auto"."""
-    dwi_no_biascorr = None
-    """DEPRECATED: see --b1-biascorrect-stage."""
-    dwi_only = False
-    """DEPRECATED: True if anat_modality is 'none'."""
-    eddy_config = None
-    """Configuration for running Eddy."""
-    fmap_bspline = None
-    """Regularize fieldmaps with a field of B-Spline basis."""
-    fmap_demean = None
-    """Remove the mean from fieldmaps."""
-    force_syn = None
-    """Run *fieldmap-less* susceptibility-derived distortions estimation."""
-    hmc_model = None
-    """Model used to generate target images for hmc."""
-    hmc_transform = None
-    """Transformation to be used in SHORELine."""
-    ignore = None
-    """Ignore particular steps for *QSIRecon*."""
     infant = False
     """Configure pipelines specifically for infant brains"""
-    intramodal_template_iters = None
-    """Number of iterations for intramodal template construction."""
-    intramodal_template_transform = None
-    """Transformation used for building the intramodal template."""
     longitudinal = False
     """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
-    no_b0_harmonization = False
-    """Skip re-scaling dwi scans to have matching b=0 intensities."""
-    output_resolution = None
-    """Isotropic voxel size for outputs."""
-    pepolar_method = None
-    """SDC method to be used for PEPOLAR fieldmaps."""
     recon_input_pipeline = None
     """Specifies which pipeline was used to preprocess data in ``recon_input``"""
     recon_spec = None
     """Recon workflow specification."""
-    separate_all_dwis = False
-    """Process all dwis separately - do not attempt concatenation."""
-    shoreline_iters = None
-    """How many iterations to run SHORELine."""
-    unringing_method = None
-    """Method for Gibbs-ringing removal. Either "none", "mrdegibbs" or "rpg"."""
-    use_syn_sdc = None
-    """Run *fieldmap-less* susceptibility-derived distortions estimation
-    in the absence of any alternatives."""
 
 
 class loggers: