Anat biascorr masks

.gitignore

@@ -104,3 +104,10 @@ notebooks/*
 .pixi/*
 !.pixi/config.toml
 .cursor/rules/cursorenv.mdc
+
+# Stray nipype interface outputs from running interfaces by hand
+/tsnr.nii.gz
+/n4_weights.nii.gz
+/template_agreement.nii.gz
+/*_bias.nii.gz
+/*.nii

qsiprep/cli/parser.py

@@ -436,6 +436,22 @@ def _bids_filter(value, parser):
         action='store_true',
         help='DEPRECATED: see --b1-biascorrect-stage',
     )
+    g_conf.add_argument(
+        '--anat-biascorrect',
+        action='store',
+        choices=['n4', 'auto', 'none'],
+        default='n4',
+        help=(
+            'Whether to run N4 bias field correction on ANATOMICAL images. '
+            'Note this is separate from --b1-biascorrect-stage, which only governs '
+            'the DWIs. '
+            '"n4" (default) always runs it; scanner-side intensity normalization '
+            '(e.g. Siemens NORM) does not remove the need for it. '
+            '"none" never runs it. '
+            '"auto" skips it when the BIDS ImageType metadata contains "NORM", '
+            'which is how Siemens and others flag console-applied normalization.'
+        ),
+    )
     g_conf.add_argument(
         '--b1-biascorrect-stage',
         action='store',
@@ -593,6 +609,24 @@ def _bids_filter(value, parser):
         'current default can be found here: '
         'https://github.com/PennLINC/qsiprep/blob/main/qsiprep/data/diffprep_params.json',
     )
+    g_moco.add_argument(
+        '--tortoise-gpu-cpu-ratio',
+        action='store',
+        type=int,
+        default=None,
+        help=(
+            'How many volumes DIFFPREP gives the GPU per pass, against one per CPU '
+            'thread, during motion and eddy correction. TORTOISE does not move the '
+            'series onto the GPU the way eddy_cuda does: it treats the GPU as one '
+            'more worker, so the number of passes is '
+            'ceil(nvolumes / (ngpus * ratio + omp-nthreads - ngpus)). '
+            'It describes the machine, not the data -- roughly how many volumes the '
+            'GPU gets through while one CPU core does one. Only worth setting when '
+            'the GPU is fast relative to the core count, since its influence falls '
+            'as --omp-nthreads rises (about 68%% of volumes at 8 cores, 19%% at 64). '
+            'Requires the patched TORTOISE. Unset leaves TORTOISE at its default of 15.'
+        ),
+    )
     g_moco.add_argument(
         '--shoreline-iters',
         action='store',

qsiprep/config.py

@@ -562,6 +562,8 @@ class workflow(_Config):
     Or make a template? Either 'iterative' or 'first'"""
     b0_to_t1w_transform = None
     """Transformation model for intramodal registration."""
+    anat_biascorrect = None
+    """Whether to N4-correct anatomicals: ``n4``, ``auto`` or ``none``."""
     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)."""
@@ -616,6 +618,8 @@ class workflow(_Config):
     """Process all dwis separately - do not attempt concatenation."""
     shoreline_iters = None
     """How many iterations to run SHORELine."""
+    tortoise_gpu_cpu_ratio = None
+    """Volumes the GPU takes per DIFFPREP pass; None leaves TORTOISE's default."""
     unringing_method = None
     """Method for Gibbs-ringing removal. Either "none", "mrdegibbs" or "rpg"."""
     use_syn_sdc = None

qsiprep/data/io_spec.json

@@ -20,7 +20,7 @@
       }
     ],
     "default_path_patterns": [
-      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|imtcoreg>}.{extension<nii|nii.gz|json>|nii.gz}",
+      "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|imtcoreg|dwiref>}.{extension<nii|nii.gz|json|tsv>|nii.gz}",
       "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5|mat>}",
       "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}]_desc-{desc}_{suffix<mask>|mask}.{extension<nii|nii.gz|json>|nii.gz}",
       "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}.{extension<nii|nii.gz|json>|nii.gz}",

qsiprep/data/unbiased_template_precise_Affine.json

@@ -0,0 +1,85 @@
+{
+    "dimension": 3,
+    "float": true,
+    "winsorize_lower_quantile": 0.002,
+    "winsorize_upper_quantile": 0.998,
+    "collapse_output_transforms": true,
+    "write_composite_transform": false,
+    "use_histogram_matching": [
+        false,
+        false
+    ],
+    "transforms": [
+        "Rigid",
+        "Affine"
+    ],
+    "number_of_iterations": [
+        [
+            1000,
+            1000
+        ],
+        [
+            1000
+        ]
+    ],
+    "output_warped_image": true,
+    "transform_parameters": [
+        [
+            0.2
+        ],
+        [
+            0.15
+        ]
+    ],
+    "convergence_threshold": [
+        1e-06,
+        1e-06
+    ],
+    "convergence_window_size": [
+        20,
+        20
+    ],
+    "metric": [
+        "Mattes",
+        "Mattes"
+    ],
+    "sampling_percentage": [
+        0.15,
+        0.2
+    ],
+    "sampling_strategy": [
+        "Random",
+        "Random"
+    ],
+    "smoothing_sigmas": [
+        [
+            8.0,
+            2.0
+        ],
+        [
+            2.0
+        ]
+    ],
+    "sigma_units": [
+        "mm",
+        "mm"
+    ],
+    "metric_weight": [
+        1.0,
+        1.0
+    ],
+    "shrink_factors": [
+        [
+            2,
+            1
+        ],
+        [
+            1
+        ]
+    ],
+    "radius_or_number_of_bins": [
+        48,
+        48
+    ],
+    "interpolation": "BSpline"
+}

qsiprep/data/unbiased_template_precise_Rigid.json

@@ -0,0 +1,63 @@
+{
+    "dimension": 3,
+    "float": true,
+    "winsorize_lower_quantile": 0.002,
+    "winsorize_upper_quantile": 0.998,
+    "collapse_output_transforms": true,
+    "write_composite_transform": false,
+    "use_histogram_matching": [
+        false
+    ],
+    "transforms": [
+        "Rigid"
+    ],
+    "number_of_iterations": [
+        [
+            1000,
+            1000
+        ]
+    ],
+    "output_warped_image": true,
+    "transform_parameters": [
+        [
+            0.2
+        ]
+    ],
+    "convergence_threshold": [
+        1e-06
+    ],
+    "convergence_window_size": [
+        20
+    ],
+    "metric": [
+        "Mattes"
+    ],
+    "sampling_percentage": [
+        0.15
+    ],
+    "sampling_strategy": [
+        "Random"
+    ],
+    "smoothing_sigmas": [
+        [
+            8.0,
+            2.0
+        ]
+    ],
+    "sigma_units": [
+        "mm"
+    ],
+    "metric_weight": [
+        1.0
+    ],
+    "shrink_factors": [
+        [
+            2,
+            1
+        ]
+    ],
+    "radius_or_number_of_bins": [
+        48
+    ],
+    "interpolation": "BSpline"
+}

qsiprep/data/unbiased_template_sloppy_Affine.json

@@ -0,0 +1,85 @@
+{
+    "dimension": 3,
+    "float": true,
+    "winsorize_lower_quantile": 0.002,
+    "winsorize_upper_quantile": 0.998,
+    "collapse_output_transforms": true,
+    "write_composite_transform": false,
+    "use_histogram_matching": [
+        false,
+        false
+    ],
+    "transforms": [
+        "Rigid",
+        "Affine"
+    ],
+    "number_of_iterations": [
+        [
+            10,
+            10
+        ],
+        [
+            10
+        ]
+    ],
+    "output_warped_image": true,
+    "transform_parameters": [
+        [
+            0.2
+        ],
+        [
+            0.15
+        ]
+    ],
+    "convergence_threshold": [
+        1e-06,
+        1e-06
+    ],
+    "convergence_window_size": [
+        20,
+        20
+    ],
+    "metric": [
+        "Mattes",
+        "Mattes"
+    ],
+    "sampling_percentage": [
+        0.05,
+        0.05
+    ],
+    "sampling_strategy": [
+        "Random",
+        "Random"
+    ],
+    "smoothing_sigmas": [
+        [
+            8.0,
+            2.0
+        ],
+        [
+            2.0
+        ]
+    ],
+    "sigma_units": [
+        "mm",
+        "mm"
+    ],
+    "metric_weight": [
+        1.0,
+        1.0
+    ],
+    "shrink_factors": [
+        [
+            2,
+            1
+        ],
+        [
+            1
+        ]
+    ],
+    "radius_or_number_of_bins": [
+        48,
+        48
+    ],
+    "interpolation": "BSpline"
+}

qsiprep/data/unbiased_template_sloppy_Rigid.json

@@ -0,0 +1,63 @@
+{
+    "dimension": 3,
+    "float": true,
+    "winsorize_lower_quantile": 0.002,
+    "winsorize_upper_quantile": 0.998,
+    "collapse_output_transforms": true,
+    "write_composite_transform": false,
+    "use_histogram_matching": [
+        false
+    ],
+    "transforms": [
+        "Rigid"
+    ],
+    "number_of_iterations": [
+        [
+            10,
+            10
+        ]
+    ],
+    "output_warped_image": true,
+    "transform_parameters": [
+        [
+            0.2
+        ]
+    ],
+    "convergence_threshold": [
+        1e-06
+    ],
+    "convergence_window_size": [
+        20
+    ],
+    "metric": [
+        "Mattes"
+    ],
+    "sampling_percentage": [
+        0.05
+    ],
+    "sampling_strategy": [
+        "Random"
+    ],
+    "smoothing_sigmas": [
+        [
+            8.0,
+            2.0
+        ]
+    ],
+    "sigma_units": [
+        "mm"
+    ],
+    "metric_weight": [
+        1.0
+    ],
+    "shrink_factors": [
+        [
+            2,
+            1
+        ]
+    ],
+    "radius_or_number_of_bins": [
+        48
+    ],
+    "interpolation": "BSpline"
+}