Changed FSL installation to just copy eddy_openmp and adjusted some eddy inputs

Author: slimnsour

.docker/fsl-6.0/bin/eddy_openmp

@@ -94,38 +94,9 @@ ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
 
 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/bin/eddy_openmp  /usr/lib/fsl/5.0/eddy_openmp
 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

Dockerfile

@@ -208,7 +208,7 @@ def _bold_reg_suffix(fallback):
     # fmt:off
     workflow.connect([
         (dwi_reference_wf, eddy_wf, [
-            ("outputnode.ref_image", "inputnode.dwi_file"),
+            ("outputnode.dwi_file", "inputnode.dwi_file"),
             ("outputnode.dwi_mask", "inputnode.dwi_mask"),
         ]),
         (inputnode, eddy_wf, [

dmriprep/workflows/dwi/base.py

@@ -110,6 +110,7 @@ def init_eddy_wf(debug=False, name="eddy_wf"):
 
     if debug:
         eddy.inputs.niter = 1
+        eddy.inputs.is_shelled = True
 
     # Generate the acqp and index files for eddy
     gen_eddy_files = pe.Node(