Faster quasiraw pipeline + mask interpolation fix

.github/workflows/testing.yml

@@ -5,7 +5,6 @@
 # .. code-block:: bash
 #
 #   $ nosetests --with-coverage --cover-package=brainprep --verbosity=2
-#     --with-doctest --doctest-options='+ELLIPSIS,+NORMALIZE_WHITESPACE'
 ###
 name: "testing[nosetests]"
 
@@ -48,7 +47,7 @@ jobs:
         python -m pip install --progress-bar off ".[ci]"
     - name: Run unit tests
       run: |
-        nosetests --with-coverage --cover-package=brainprep --verbosity=2 --with-doctest --doctest-options='+ELLIPSIS,+NORMALIZE_WHITESPACE'
+        nosetests --with-coverage --cover-package=brainprep --verbosity=2
     - name: Coveralls
       if: matrix.python-version == 3.12
       env:

CHANGELOG.rst

@@ -10,12 +10,12 @@ NEW
 ---
 
 - :bdg-success:`Enhancement` Add the dmriprep workflow.
-- :bdg-success:`Enhancement` Add the mrophologist workflow.
+- :bdg-success:`Enhancement` Add the morphologist workflow.
 
 Fixes
 -----
 
-- :bdg-danger:`Deprecation` Fix the containers that are using mri_synthstrip.
+- :bdg-danger:`Deprecation` Fix the containers that are using `mri_synthstrip`.
 - :bdg-danger:`Deprecation` The run mapping file has been moved to avoid
   conflicts with FreeSurfer.
 
@@ -24,10 +24,15 @@ Enhancements
 
 - :bdg-success:`Enhancement` Add signature hook.
 - :bdg-success:`Enhancement` Add live comand line monitoring support.
+- :bdg-success:`Enhancement` Support multi-modality in Quasi-Raw workflow.
+- :bdg-success:`Enhancement` Add `quick` mode in Quasi-Raw workflow.
+- :bdg-success:`Enhancement` Support multi-modality in Deface workflow.
 
 Changes
 -------
 
+- :bdg-danger:`Deprecation` Optimize the Quasi-Raw workflow steps.
+
 
 2.0.0
 =====

brainprep/decorators.py

@@ -65,16 +65,6 @@ class Hook:
     ``before_call`` returns the inputs unchanged, and ``after_call`` returns
     the outputs unchanged.
 
-    Methods
-    -------
-    before_call(func, inputs)
-        Hook executed before the wrapped function is called.
-        Must return a dictionary of (possibly modified) inputs.
-
-    after_call(func, outputs)
-        Hook executed after the wrapped function returns.
-        Must return the (possibly modified) output value.
-
     Notes
     -----
     Subclasses may override one or both methods. If a method is not
@@ -87,14 +77,22 @@ def before_call(
             func: Callable,
             inputs: dict[str, Any],
         ) -> dict[str, Any]:
-        """Transform and inspect inputs before the function call."""
+        """
+        Hook executed before the wrapped function is called.
+        Transform and/or inspect inputs.
+        Must return a dictionary of (possibly modified) inputs.
+        """
         return inputs
 
     def after_call(
             self,
             outputs: Any,
         ) -> Any:
-        """Transform and inspect outputs after the function call."""
+        """
+        Hook executed after the wrapped function returns.
+        Transform and/or inspect outputs.
+        Must return the (possibly modified) output value.
+        """
         return outputs
 
 

brainprep/interfaces/__init__.py

@@ -79,6 +79,7 @@
     fmriprep_metrics,
     incremental_pca,
     mask_overlap,
+    maskdiff,
     mean_correlation,
     mriqc_metrics,
     network_entropy,
@@ -91,7 +92,6 @@
 from .utils import (
     anonfile,
     copyfiles,
-    maskdiff,
     movedir,
     ungzfile,
     write_uuid_mapping,

brainprep/interfaces/ants.py

@@ -40,7 +40,8 @@ def biasfield(
         image_file: File,
         mask_file: File,
         output_dir: Directory,
-        entities: dict) -> tuple[list[str], tuple[File]]:
+        entities: dict,
+        quick: bool = False) -> tuple[list[str], tuple[File]]:
     """
     Bias field correction of a BIDS-compliant anatomical image using ANTs's
     `N4BiasFieldCorrection`.
@@ -55,6 +56,10 @@ def biasfield(
         Directory where the reoriented image will be saved.
     entities : dict
         A dictionary of parsed BIDS entities including modality.
+    quick : bool
+        Increased shrink factor from `1` to `4`, which downsamples the image
+        before estimating the bias field.
+        Default False.
 
     Returns
     -------
@@ -73,7 +78,7 @@ def biasfield(
         "N4BiasFieldCorrection",
         "-d", "3",
         "-i", str(image_file),
-        "-s", "1",
+        "-s", "4" if quick else "1",
         "-b", "[1x1x1,3]",
         "-c", "[50x50x50x50,0.001]",
         "-t", "[0.15,0.01,200]",

brainprep/interfaces/freesurfer.py

@@ -77,25 +77,29 @@ def brainmask(
     command : list[str]
         Skull-stripping command-line.
     outputs : tuple[File]
-        - mask_file : File - Skull-stripped brain image file.
+        -brain_file : File - Skull-stripped brain image file.
+        -mask_file : File - Binary brain mask image file.
 
     References
     ----------
 
     .. footbibliography::
     """
-    basename = "sub-{sub}_ses-{ses}_run-{run}_mod-{mod}_brainmask".format(
+    basename = "sub-{sub}_ses-{ses}_run-{run}_mod-{mod}".format(
         **entities)
-    mask_file = output_dir / f"{basename}.nii.gz"
+    brain_file = output_dir / f"{basename}_brain.nii.gz"
+    mask_file = output_dir / f"{basename}_brainmask.nii.gz"
 
     command = [
         "mri_synthstrip",
         "-i", str(image_file),
+        "-o", str(brain_file),
         "-m", str(mask_file),
+        "-f", "0",
         "--no-csf",
     ]
 
-    return command, (mask_file, )
+    return command, (brain_file, mask_file, )
 
 
 @step(

brainprep/interfaces/fsl.py

@@ -12,6 +12,7 @@
 """
 
 import os
+from pathlib import Path
 
 from ..decorators import (
     CoerceparamsHook,
@@ -61,7 +62,7 @@ def reorient(
     outputs : tuple[File]
         - reorient_image_file : File - Reoriented input image file.
     """
-    basename = "sub-{sub}_ses-{ses}_run-{run}_mod-T1w_reorient".format(
+    basename = "sub-{sub}_ses-{ses}_run-{run}_mod-{mod}_reorient".format(
         **entities)
     reorient_image_file = output_dir / f"{basename}.nii.gz"
 
@@ -109,7 +110,8 @@ def deface(
     outputs : tuple[File | list[File]]
         - deface_file : File - Defaced input T1w image file.
         - mask_file : File - Defacing binary mask.
-        - vol_files : list[File] - Defacing 3d rendering.
+        - transform_file : File - Affine transformation from original space to
+          MNI152 space.
 
     Raises
     ------
@@ -126,17 +128,29 @@ def deface(
         **entities)
     deface_file = output_dir / f"{basename}.nii.gz"
     mask_file = output_dir / f"{basename}mask.nii.gz"
-
-    command = [
-        "fsl_deface",
-        str(t1_file),
-        str(deface_file),
-        "-d", str(mask_file),
-        "-f", "0.5",
-        "-B",
+    transform_file = output_dir / f"{basename}affine.mat"
+
+    resource_dir = Path(__file__).parent.parent / "resources"
+    bigfov_transfrom_file = resource_dir / "MNI_BigFov_to_MNI.mat"
+
+    commands = [
+        [
+            "fsl_deface",
+            str(t1_file),
+            str(deface_file),
+            "-d", str(mask_file),
+            "-m13", str(transform_file),
+            "-f", "0.5",
+            "-B",
+        ],
+        [
+            "convert_xfm",
+            "-omat", str(transform_file),
+            "-concat", str(bigfov_transfrom_file), str(transform_file),
+        ]
     ]
 
-    return command, (deface_file, mask_file, )
+    return commands, (deface_file, mask_file, transform_file)
 
 
 @step(
@@ -206,7 +220,8 @@ def scale(
         image_file: File,
         scale: int,
         output_dir: Directory,
-        entities: dict) -> tuple[list[str], tuple[File]]:
+        entities: dict,
+        interpolation: str = "spline") -> tuple[list[str], tuple[File]]:
     """
     Apply an isotropic resampling transformation to a BIDS-compliant image
     file using FSL's `flirt`.
@@ -221,6 +236,10 @@ def scale(
         Directory where the scaled image will be saved.
     entities : dict
         A dictionary of parsed BIDS entities including modality.
+    interpolation: str
+        The interpolation method: 'trilinear', 'nearestneighbour', 'sinc', or
+        'spline'.
+        Default 'spline'.
 
     Returns
     -------
@@ -240,6 +259,7 @@ def scale(
         "-in", str(image_file),
         "-ref", str(image_file),
         "-applyisoxfm", str(scale),
+        "-interp", interpolation,
         "-out", str(scaled_anatomical_file),
         "-omat", str(transform_file),
         "-verbose", "1",
@@ -263,7 +283,9 @@ def affine(
         anatomical_file: File,
         template_file: File,
         output_dir: Directory,
-        entities: dict) -> tuple[list[str], tuple[File]]:
+        entities: dict,
+        rigid: bool = False,
+        quick: bool = False) -> tuple[list[str], tuple[File]]:
     """
     Affinely register a BIDS-compliant anatomical image to a template file
     using FSL's `flirt`.
@@ -278,6 +300,15 @@ def affine(
         Directory where the affine transformation will be saved.
     entities : dict
         A dictionary of parsed BIDS entities including modality.
+    rigid : bool
+        Estimate a 6 DOF transformation that maintains the original size and
+        shape of the brain. By default a 9 DOF transformation allows for
+        additional scaling in the x, y, and z directions, adjusting the size
+        and shape of the brain during the alignment process.
+        Default False.
+    quick : bool
+        Restricted rotation search range to +/-30° on all three axes.
+        Default False.
 
     Returns
     -------
@@ -301,11 +332,17 @@ def affine(
         "-anglerep", "euler",
         "-bins", "256",
         "-interp", "trilinear",
-        "-dof", "9",
+        "-dof", "6" if rigid else "9",
         "-out", str(aligned_anatomical_file),
         "-omat", str(transform_file),
         "-verbose", "1"
     ]
+    if quick:
+        command += [
+            "-searchrx", "-30", "30",
+            "-searchry", "-30", "30",
+            "-searchrz", "-30", "30",
+        ]
 
     return command, (aligned_anatomical_file, transform_file)
 
@@ -346,7 +383,8 @@ def applyaffine(
         A dictionary of parsed BIDS entities including modality.
     interpolation: str
         The interpolation method: 'trilinear', 'nearestneighbour', 'sinc', or
-        'spline'. Default 'spline'.
+        'spline'.
+        Default 'spline'.
 
     Returns
     -------
@@ -364,7 +402,7 @@ def applyaffine(
         "-in", str(image_file),
         "-ref", str(template_file),
         "-init", str(transform_file),
-        "-interp", str(interpolation),
+        "-interp", interpolation,
         "-applyxfm",
         "-out", str(aligned_image_file),
     ]