Merge pull request #7 from GalKepler/eddy_fsl

found a way around dwifslpreproc
GalKepler · Jul 24, 2024 · fa0213f · fa0213f
2 parents 41ab300 + 30d55af
commit fa0213f
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Showing 4 changed files with 45 additions and 5 deletions.
diff --git a/src/keprep/interfaces/bids.py b/src/keprep/interfaces/bids.py
@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from pathlib import Path
-from typing import Union
 
 from bids import BIDSLayout
 from bids.layout import Query, parse_file_entities
@@ -19,7 +18,8 @@
 LOGGER = logging.getLogger("nipype.interface")
 
 CUSTOM_PATH_PATTERNS = [
-    "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi|dwiref|epiref|lowb|dseg|streamlines>}{extension<.json|.nii.gz|.nii|.tck|.trk>|.nii.gz}"  # pylint: disable=line-too-long
+    "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi|dwiref|epiref|lowb|dseg|streamlines>}{extension<.json|.nii.gz|.nii|.tck|.trk>|.nii.gz}",  # pylint: disable=line-too-long
+    "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/{desc}",
 ]
 
 

diff --git a/src/keprep/workflows/dwi/stages/derivatives.py b/src/keprep/workflows/dwi/stages/derivatives.py
@@ -7,6 +7,16 @@
 DWI_PREPROC_BASE_ENTITIES = dict(desc="preproc", space="dwi", datatype="dwi")
 
 
+def _eddy_qc_dds(eddy_qc, source_file):
+    import shutil
+    from pathlib import Path
+
+    destination = Path(source_file).parent / "eddy_qc"
+    if destination.exists():
+        shutil.rmtree(destination)
+    shutil.copytree(eddy_qc, destination)
+
+
 def init_derivatives_wf(name: str = "derivatives_wf") -> pe.Workflow:
     """
     Build the workflow that saves derivatives.
@@ -39,6 +49,7 @@ def init_derivatives_wf(name: str = "derivatives_wf") -> pe.Workflow:
                 "dwi2t1w_aff",
                 "t1w2dwi_aff",
                 "dwi_brain_mask",
+                "eddy_qc",
                 "sdc_report",
                 "coreg_report",
                 "unsifted_tck",
@@ -48,6 +59,16 @@ def init_derivatives_wf(name: str = "derivatives_wf") -> pe.Workflow:
         name="inputnode",
     )
 
+    ds_eddy_qc = pe.Node(
+        niu.Function(
+            input_names=["eddy_qc", "source_file"],
+            output_names=[],
+            function=_eddy_qc_dds,
+        ),
+        name="ds_eddy_qc",
+        run_without_submitting=True,
+    )
+
     ds_sdc_report = pe.Node(
         DerivativesDataSink(
             base_directory=output_dir,
@@ -194,6 +215,16 @@ def init_derivatives_wf(name: str = "derivatives_wf") -> pe.Workflow:
 
     workflow.connect(
         [
+            (
+                inputnode,
+                ds_eddy_qc,
+                [("eddy_qc", "eddy_qc")],
+            ),
+            (
+                ds_dwi_preproc,
+                ds_eddy_qc,
+                [("out_file", "source_file")],
+            ),
             (
                 inputnode,
                 ds_sdc_report,

diff --git a/src/keprep/workflows/dwi/stages/eddy.py b/src/keprep/workflows/dwi/stages/eddy.py
@@ -35,7 +35,9 @@ def init_eddy_wf(name: str = "eddy_wf") -> pe.Workflow:
     )
 
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=["dwi_preproc", "dwi_reference_distorted"]),
+        niu.IdentityInterface(
+            fields=["dwi_preproc", "dwi_reference_distorted", "eddy_qc"]
+        ),
         name="outputnode",
     )
 
@@ -156,6 +158,7 @@ def init_eddy_wf(name: str = "eddy_wf") -> pe.Workflow:
                 outputnode,
                 [
                     ("out_file", "dwi_preproc"),
+                    ("eddyqc_all", "eddy_qc"),
                 ],
             ),
         ]

diff --git a/src/keprep/workflows/dwi/workflow.py b/src/keprep/workflows/dwi/workflow.py
@@ -1,5 +1,4 @@
 from pathlib import Path
-from typing import Union
 
 from bids import BIDSLayout
 from nipype.interfaces import utility as niu
@@ -71,7 +70,7 @@ def init_dwi_preproc_wf(dwi_file: str | Path, subject_data: dict):
     inputnode.inputs.fmap_bval = Path(layout.get_bval(fieldmap))
     inputnode.inputs.fmap_json = Path(layout.get_nearest(fieldmap, extension="json"))
 
-    outputnode = pe.Node(
+    outputnode = pe.Node(  # noqa: F841
         niu.IdentityInterface(
             fields=["dwi_preproc", "dwi_reference", "dwi_mask"],
         ),
@@ -283,6 +282,13 @@ def init_dwi_preproc_wf(dwi_file: str | Path, subject_data: dict):
                     ("dwi_file", "inputnode.source_file"),
                 ],
             ),
+            (
+                eddy_wf,
+                ds_workflow,
+                [
+                    ("outputnode.eddy_qc", "inputnode.eddy_qc"),
+                ],
+            ),
             (
                 post_eddy,
                 ds_workflow,