Keeping track of fMRIPrep.

.gitignore

@@ -107,3 +107,8 @@ ENV/
 
 #kubernetes stuff
 kubernetes/jobs/
+
+# Local tests
+dmriprep/data/tests/local
+*.ipynb
+run_tests.py

dmriprep/cli/parser.py

@@ -23,20 +23,20 @@
 """Parser."""
 import os
 import sys
+
 from .. import config
 
 
 def _build_parser():
     """Build parser object."""
+    from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
     from functools import partial
     from pathlib import Path
-    from argparse import (
-        ArgumentParser,
-        ArgumentDefaultsHelpFormatter,
-    )
+
+    from niworkflows.utils.spaces import OutputReferencesAction, Reference
     from packaging.version import Version
+
     from .version import check_latest, is_flagged
-    from niworkflows.utils.spaces import Reference, OutputReferencesAction
 
     def _path_exists(path, parser):
         """Ensure a given path exists."""
@@ -52,7 +52,7 @@ def _min_one(value, parser):
         return value
 
     def _to_gb(value):
-        scale = {"G": 1, "T": 10 ** 3, "M": 1e-3, "K": 1e-6, "B": 1e-9}
+        scale = {"G": 1, "T": 10**3, "M": 1e-3, "K": 1e-6, "B": 1e-9}
         digits = "".join([c for c in value if c.isdigit()])
         units = value[len(digits) :] or "M"
         return int(digits) * scale[units[0]]
@@ -70,7 +70,11 @@ def _bids_filter(value):
     verstr = f"dMRIPrep v{config.environment.version}"
     currentv = Version(config.environment.version)
     is_release = not any(
-        (currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease)
+        (
+            currentv.is_devrelease,
+            currentv.is_prerelease,
+            currentv.is_postrelease,
+        )
     )
 
     parser = ArgumentParser(
@@ -96,7 +100,8 @@ def _bids_filter(value):
         "output_dir",
         action="store",
         type=Path,
-        help="the output path for the outcomes of preprocessing and visual " "reports",
+        help="the output path for the outcomes of preprocessing and visual "
+        "reports",
     )
     parser.add_argument(
         "analysis_level",
@@ -181,7 +186,9 @@ def _bids_filter(value):
         help="nipype plugin configuration file",
     )
     g_perfm.add_argument(
-        "--anat-only", action="store_true", help="run anatomical workflows only"
+        "--anat-only",
+        action="store_true",
+        help="run anatomical workflows only",
     )
     g_perfm.add_argument(
         "--boilerplate_only",
@@ -249,7 +256,9 @@ def _bids_filter(value):
     )
 
     #  ANTs options
-    g_ants = parser.add_argument_group("Specific options for ANTs registrations")
+    g_ants = parser.add_argument_group(
+        "Specific options for ANTs registrations"
+    )
     g_ants.add_argument(
         "--skull-strip-template",
         default="OASIS30ANTs",
@@ -264,7 +273,9 @@ def _bids_filter(value):
     )
 
     # SyN-unwarp options
-    g_syn = parser.add_argument_group("Specific options for SyN distortion correction")
+    g_syn = parser.add_argument_group(
+        "Specific options for SyN distortion correction"
+    )
     g_syn.add_argument(
         "--use-syn-sdc",
         action="store_true",
@@ -287,7 +298,9 @@ def _bids_filter(value):
     )
 
     # FreeSurfer options
-    g_fs = parser.add_argument_group("Specific options for FreeSurfer preprocessing")
+    g_fs = parser.add_argument_group(
+        "Specific options for FreeSurfer preprocessing"
+    )
     g_fs.add_argument(
         "--fs-license-file",
         metavar="PATH",
@@ -415,11 +428,14 @@ def _bids_filter(value):
 def parse_args(args=None, namespace=None):
     """Parse args and run further checks on the command line."""
     import logging
+
     from niworkflows.utils.spaces import Reference, SpatialReferences
 
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)
-    config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
+    config.execution.log_level = int(
+        max(25 - 5 * opts.verbose_count, logging.DEBUG)
+    )
     config.from_dict(vars(opts))
     config.loggers.init()
 
@@ -469,18 +485,33 @@ def parse_args(args=None, namespace=None):
     output_dir = config.execution.output_dir
     work_dir = config.execution.work_dir
     version = config.environment.version
+    output_layout = config.execution.output_layout
 
     if config.execution.fs_subjects_dir is None:
         config.execution.fs_subjects_dir = output_dir / "freesurfer"
-
+    if config.execution.fs_subjects_dir is None:
+        if output_layout == "bids":
+            config.execution.fs_subjects_dir = (
+                output_dir / "sourcedata" / "freesurfer"
+            )
+        elif output_layout == "legacy":
+            config.execution.fs_subjects_dir = output_dir / "freesurfer"
+    if config.execution.dmriprep_dir is None:
+        if output_layout == "bids":
+            config.execution.dmriprep_dir = output_dir
+        elif output_layout == "legacy":
+            config.execution.dmriprep_dir = output_dir / "dmriprep"
     # Wipe out existing work_dir
     if opts.clean_workdir and work_dir.exists():
         from niworkflows.utils.misc import clean_directory
 
-        build_log.log("Clearing previous dMRIPrep working directory: %s", work_dir)
+        build_log.log(
+            "Clearing previous dMRIPrep working directory: %s", work_dir
+        )
         if not clean_directory(work_dir):
             build_log.warning(
-                "Could not clear all contents of working directory: %s", work_dir
+                "Could not clear all contents of working directory: %s",
+                work_dir,
             )
 
     # Ensure input and output folders are not the same
@@ -533,4 +564,6 @@ def parse_args(args=None, namespace=None):
         )
 
     config.execution.participant_label = sorted(participant_label)
-    config.workflow.skull_strip_template = config.workflow.skull_strip_template[0]
+    config.workflow.skull_strip_template = (
+        config.workflow.skull_strip_template[0]
+    )