Scaling cli

.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/fmriprep.py

@@ -14,6 +14,7 @@
 import json
 import os
 import shutil
+import tempfile
 from pathlib import Path
 
 import numpy as np
@@ -40,6 +41,7 @@
     File,
 )
 from ..utils import (
+    print_warn,
     sidecar_from_file,
 )
 
@@ -106,14 +108,33 @@ def fmriprep_wf(
     Notes
     -----
     - Creates BIDS subject specific working directory using copy in
-      'rawdata'.
+      'rawdata' folder.
+    - Create FreeSurfer subject directory using copy in 'freesurfer' folder.
+    - To avoid paths that are too long and not allowed by FreeSurfer, use the
+      '/tmp' directory. To prevent data leakage, please bind '/tmp' to a
+      secure location.
     - Store intermediate pre-processing outputs in 'work'.
+    - Use as many CPUs as available.
     """
     rawdata_dir = workspace_dir / "rawdata"
     anat_dir = rawdata_dir / "anat"
     func_dir = rawdata_dir / "func"
     work_dir = workspace_dir / "work"
-    for path in (anat_dir, func_dir, work_dir):
+    work_freesurfer_dir = workspace_dir / "freesurfer"
+    tmp_dir = Path(tempfile.TemporaryDirectory().name)
+    work_tmp_dir = tmp_dir / "work"
+    print_warn(
+        "To avoid paths that are too long and not allowed by FreeSurfer, we "
+        "use the '/tmp' directory. To prevent data leakage, please bind "
+        "'/tmp' to a secure location. Current temporary directory: "
+        f"{tmp_dir}."
+    )
+    for path in (
+            anat_dir,
+            func_dir,
+            work_freesurfer_dir,
+            work_tmp_dir,
+        ):
         path.mkdir(parents=True, exist_ok=True)
     subject, session = entities["sub"], entities["ses"]
     fshome_dir = os.getenv("FREESURFER_HOME")
@@ -122,6 +143,8 @@ def fmriprep_wf(
             "You must define the 'FREESURFER_HOME' environment variable."
         )
     fshome_dir = Path(fshome_dir)
+    fssubject_dir = freesurfer_dir / f"sub-{subject}"
+    fssubject_local_dir = work_freesurfer_dir / f"sub-{subject}_ses-{session}"
 
     for source_file, target_dir in zip(
             [t1_file, *func_files],
@@ -174,10 +197,18 @@ def fmriprep_wf(
             (
                 fmriprep_dir /
                 "func" /
-                f"{basename}_space-{template}_den-91k_bold.dtseries.nii",
+                f"{basename}_hemi-L_space-fsnative_bold.func.gii",
+            ),
+            (
+                fmriprep_dir /
+                "func" /
+                f"{basename}_hemi-R_space-fsnative_bold.func.gii",
+            ),
+            (
+                fmriprep_dir /
+                "func" /
+                f"{basename}_space-fsLR_den-91k_bold.dtseries.nii",
             )
-            for template in ("fsnative",
-                             "fsLR")
         ]
         confounds_file = (
             fmriprep_dir /
@@ -191,30 +222,49 @@ def fmriprep_wf(
             confounds_file,
         ])
 
-    command = [
-        "fmriprep",
-        str(rawdata_dir),
-        str(output_dir.parent.parent),
-        "participant",
-        "--fs-subjects-dir", str(freesurfer_dir),
-        "--work-dir", str(work_dir),
-        "--n-cpus", str(os.cpu_count()),
-        "--stop-on-first-crash",
-        "--fs-license-file", str(fshome_dir / "license.txt"),
-        "--skip-bids-validation",
-        "--fs-no-reconall",
-        "--fs-no-resume",
-        "--force", "bbr", "syn-sdc",
-        "--no-msm",
-        "--cifti-output", "91k",
-        "--output-spaces",
-        "T1w", "MNI152NLin2009cAsym", "MNI152NLin2009cAsym:res-2",
-        "fsnative", "fsLR",
-        "--ignore", "slicetiming",
-        "--participant-label", subject,
+    commands = [
+        [
+            "cp",
+            "-r",
+            str(fssubject_dir),
+            str(fssubject_local_dir),
+        ],
+        [
+            "fmriprep",
+            str(rawdata_dir),
+            str(output_dir.parent.parent),
+            "participant",
+            "--notrack",
+            "--skip-bids-validation",
+            "--stop-on-first-crash",
+            "--n-cpus", str(os.cpu_count()),
+            "--fs-license-file", str(fshome_dir / "license.txt"),
+            "--fs-subjects-dir", str(work_freesurfer_dir),
+            "--work-dir", str(work_tmp_dir),
+            "--fs-no-resume",
+            "--force", "bbr", "syn-sdc",
+            "--no-msm",
+            "--cifti-output", "91k",
+            "--output-spaces",
+            "T1w", "MNI152NLin2009cAsym", "MNI152NLin2009cAsym:res-2",
+            "fsnative", "fsLR",
+            "--ignore", "slicetiming",
+            "--participant-label", subject,
+        ],
+        [
+            "cp",
+            "-r",
+            str(work_tmp_dir),
+            str(work_dir.parent),
+        ],
+        [
+            "rm",
+            "-r",
+            str(tmp_dir),
+        ],
     ]
 
-    return command, (rfmri_outputs, qc_file)
+    return commands, (rfmri_outputs, qc_file)
 
 
 @step(

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(