Changed fsl version to 5.0.11 and switched from eddy_correct to eddy_openmp

Author: slimnsour

Dockerfile

@@ -96,6 +96,36 @@ COPY .docker/fsl-6.0/bin/topup /usr/share/fsl/5.0/bin/topup
 COPY .docker/fsl-6.0/bin/imglob /usr/share/fsl/5.0/bin/imglob
 COPY .docker/fsl-6.0/lib/* /usr/lib/fsl/5.0/
 
+ENV FSLDIR="/opt/fsl-5.0.11" \
+    PATH="/opt/fsl-5.0.11/bin:$PATH" \
+    FSLOUTPUTTYPE="NIFTI_GZ"
+
+RUN apt-get update -qq && \
+    apt-get install -y -q --no-install-recommends \
+           bc \
+           dc \
+           file \
+           libfontconfig1 \
+           libfreetype6 \
+           libgl1-mesa-dev \
+           libglu1-mesa-dev \
+           libgomp1 \
+           libice6 \
+           libxcursor1 \
+           libxft2 \
+           libxinerama1 \
+           libxrandr2 \
+           libxrender1 \
+           libxt6 \
+           python \
+           wget && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* && \
+    echo "Downloading FSL ..." && \
+    wget -q http://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py && \
+    chmod 775 fslinstaller.py && \
+    /usr/bin/python fslinstaller.py -d /opt/fsl-5.0.11 -V 5.0.11 -q
+
 # Installing ANTs 2.3.3 (NeuroDocker build)
 # Note: the URL says 2.3.4 but it is actually 2.3.3
 ENV ANTSPATH=/usr/lib/ants

dmriprep/workflows/dwi/base.py

@@ -203,12 +203,18 @@ def _bold_reg_suffix(fallback):
         # fmt: on
 
     # Eddy distortion correction
-    eddy_wf = init_eddy_wf()
+    eddy_wf = init_eddy_wf(debug=config.execution.debug)
+    eddy_wf.inputs.inputnode.metadata = layout.get_metadata(str(dwi_file))
     # fmt:off
     workflow.connect([
         (dwi_reference_wf, eddy_wf, [
             ("outputnode.ref_image", "inputnode.dwi_file"),
-        ])
+            ("outputnode.dwi_mask", "inputnode.dwi_mask"),
+        ]),
+        (inputnode, eddy_wf, [
+            ("in_bvec", "inputnode.in_bvec"),
+            ("in_bval", "inputnode.in_bval")
+        ]),
     ])
     # fmt:on
 

dmriprep/workflows/dwi/eddy.py

@@ -52,7 +52,7 @@ def gen_eddy_textfiles(in_file, in_meta):
     return out_acqparams, out_index
 
 
-def init_eddy_wf(name="eddy_wf"):
+def init_eddy_wf(debug=False, name="eddy_wf"):
     """
     Create a workflow for head-motion & Eddy currents distortion estimation with FSL.
 
@@ -72,26 +72,71 @@ def init_eddy_wf(name="eddy_wf"):
         The eddy corrected diffusion image..
 
     """
-    from nipype.interfaces.fsl import EddyCorrect
-
-    inputnode = pe.Node(niu.IdentityInterface(fields=["dwi_file"]), name="inputnode",)
+    from nipype.interfaces.fsl import Eddy
+
+    inputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=[
+                "dwi_file",
+                "metadata",
+                "dwi_mask",
+                "in_bvec",
+                "in_bval"
+            ]
+        ),
+        name="inputnode",
+    )
 
-    outputnode = pe.Node(niu.IdentityInterface(fields=["out_eddy"]), name="outputnode",)
+    outputnode = pe.Node(
+        niu.IdentityInterface(
+            fields=[
+                "out_rotated_bvecs",
+                "out_eddy"
+            ]
+        ),
+        name="outputnode",
+    )
 
     workflow = Workflow(name=name)
     workflow.__desc__ = f"""\
 Geometrical distortions derived from the so-called Eddy-currents, and head-motion
-realignment parameters were estimated with the joint modeling of ``eddy_correct``,
-included in FSL {EddyCorrect().version} [@eddy].
+realignment parameters were estimated with the joint modeling of ``eddy_openmp``,
+included in FSL {Eddy().version} [@eddy].
 """
+    eddy = pe.Node(
+        Eddy(repol=True, cnr_maps=True, residuals=True, method="jac"),
+        name="eddy",
+    )
 
-    eddy_correct = pe.Node(EddyCorrect(), name="eddy_correct",)
+    if debug:
+        eddy.inputs.niter = 1
+
+    # Generate the acqp and index files for eddy
+    gen_eddy_files = pe.Node(
+        niu.Function(
+            input_names=["in_file", "in_meta"],
+            output_names=["out_acqparams", "out_index"],
+            function=gen_eddy_textfiles,
+        ),
+        name="gen_eddy_files",
+    )
 
-    # Connect the workflow
     # fmt:off
     workflow.connect([
-        (inputnode, eddy_correct, [("dwi_file", "in_file")]),
-        (eddy_correct, outputnode, [("eddy_corrected", "out_eddy")]),
+        (inputnode, eddy, [
+            ("dwi_file", "in_file"),
+            ("dwi_mask", "in_mask"),
+            ("in_bvec", "in_bvec"),
+            ("in_bval", "in_bval"),
+        ]),
+        (inputnode, gen_eddy_files, [
+            ("dwi_file", "in_file"),
+            ("metadata", "in_meta")
+        ]),
+        (eddy, outputnode, [
+            ("out_corrected", "out_eddy"),
+            ("out_rotated_bvecs", "out_rotated_bvecs")
+        ]),
     ])
     # fmt:on
     return workflow