fix: pointing to a different nipype commit with fixes for topup odd num slices

Author: akeshavan

dmriprep/run.py

@@ -364,6 +364,12 @@ def get_dmriprep_pe_workflow():
     import multiprocessing
     eddy.inputs.num_threads = multiprocessing.cpu_count()
 
+    topup = prep.get_node('peb_correction.topup')
+    topup.inputs.checksize = True
+
+    applytopup = prep.get_node('peb_correction.unwarp')
+    applytopup.inputs.checksize = True
+
     eddy_quad = pe.Node(fsl.EddyQuad(verbose=True), name="eddy_quad")
     get_path = lambda x: x.split('.nii.gz')[0]
     wf.connect(prep, ('fsl_eddy.out_corrected', get_path), eddy_quad, "base_name")

docker/environment.yml

@@ -11,7 +11,7 @@ dependencies:
    - pandas
    - tqdm
    - pip:
-     - "--editable=git+https://github.com/akeshavan/nipype@7b5e7ab92183eb561980ec713d86eb69f28733e1#egg=nipype"
+     - "--editable=git+https://github.com/akeshavan/nipype@a9520619057120478f0fb9d6fa719c2da32ec4e7#egg=nipype"
      - "--editable=git+https://git.fmrib.ox.ac.uk/matteob/eddy_qc_release@57bb11da6a634c4195593fbc439ba9f8998157b0#egg=eddy_qc"
      - bids
      - duecredit

kubernetes/run_dmriprep.yml.tmpl

@@ -9,5 +9,9 @@ spec:
       - name: dmriprep-subject
         image: gcr.io/dmriprep/dmriprep:kube3
         command: ["/neurodocker/startup.sh", "./dmriprep_all.sh",  "{{subject}}", "{{access_key}}", "{{secret_key}}"]
+        resources:
+          requests:
+            memory: "6G"
+            cpu: "1"
       restartPolicy: Never
   backoffLimit: 1