fix: updated docker with latest nipype, to run eddy with cnr and residuals output

Author: akeshavan

dmriprep/run.py

@@ -1,4 +1,5 @@
 import os.path as op
+import os
 from shutil import copyfile
 
 
@@ -357,6 +358,10 @@ def get_dmriprep_pe_workflow():
 
     eddy = prep.get_node('fsl_eddy')
     eddy.inputs.repol = True
+    eddy.inputs.cnr_maps = True
+    eddy.inputs.residuals = True
+    import multiprocessing
+    eddy.inputs.num_threads = multiprocessing.cpu_count()
 
     def id_outliers_fn(outlier_report, threshold, dwi_file):
         """Get list of scans that exceed threshold for number of outliers
@@ -669,6 +674,10 @@ def binarize_aparc(aparc_aseg):
                datasink, "dmriprep.qc.@eddyparamsshellalign")
     wf.connect(prep, "fsl_eddy.out_parameter",
                datasink, "dmriprep.qc.@eddyparams")
+    wf.connect(prep, "fsl_eddy.out_cnr_maps",
+               datasink, "dmriprep.qc.@eddycndr")
+    wf.connect(prep, "fsl_eddy.out_residuals",
+               datasink, "dmriprep.qc.@eddyresid")
 
     # the file that told us which volumes to trop
     wf.connect(id_outliers_node, "outpath", datasink, "dmriprep.qc.@droppedscans")

docker/Dockerfile

@@ -132,14 +132,14 @@ RUN apt-get update -qq \
 
 COPY ./license.txt /opt/freesurfer-6.0.0/license.txt
 
+#&& sync && conda clean -tipsy && sync
+RUN apt-get install -y libopenblas-base
+ENV LD_LIBRARY_PATH=/usr/lib/openblas-base/
+
 ADD environment.yml environment.yml
 RUN apt-get update && apt-get install -y git gcc
 RUN conda env create -f environment.yml
 
-#&& sync && conda clean -tipsy && sync
-RUN apt-get install libopenblas-base
-ENV LD_LIBRARY_PATH=/usr/lib/openblas-base/
-
 RUN sed -i '$isource activate dmriprep' $ND_ENTRYPOINT
 
 

docker/environment.yml

@@ -11,6 +11,6 @@ dependencies:
    - pandas
    - tqdm
    - pip:
-     - "--editable=git+https://github.com/nipy/nipype@fa0a101fec2d010dcb68910000f66d7c64e5d03e#egg=nipype"
+     - "--editable=git+https://github.com/nipy/nipype@35b58cdb59a900430f4b9639e220c8408341805d#egg=nipype"
      - bids
      - duecredit