fix: updated qc to connect eddy_quad to report.json

Author: akeshavan

dmriprep/data.py

@@ -425,6 +425,16 @@ def postprocess(self, subject):
                             stdout=fnull,
                             stderr=subprocess.STDOUT)
 
+            # if the site is CBIC, then the freesurfer directory has an additional level.
+            # move that level up by 1 (e.g. removing the T1w_VNavNorm folder
+            if subject.site == 'Site-CBIC':
+                newpath = freesurfer_path.replace('T1w_VNavNorm/', '')
+                move_cmd = 'mv {oldpath} {newpath}'.format(oldpath=freesurfer_path, newpath=newpath)
+                fnull1 = open(os.devnull, 'w')
+                subprocess.call(move_cmd.split(),
+                                stdout=fnull1,
+                                stderr=subprocess.STDOUT)
+
 
 class Subject:
     """A single dMRI study subject"""

dmriprep/qc.py

@@ -3,7 +3,7 @@
 import os.path as op
 from dipy.segment.mask import median_otsu
 from io import BytesIO
-from nipype.utils.filemanip import save_json
+from nipype.utils.filemanip import save_json, load_json
 import base64
 import matplotlib
 matplotlib.use('agg')
@@ -212,6 +212,7 @@ def createB0_ColorFA_Mask_Sprites(b0_file, colorFA_file, mask_file):
 def create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
                        color_fa_file, anat_mask_file,
                        outlier_indices,
+                       eddy_qc_file,
                        outpath=op.abspath('./report.json')):
 
     report = {}
@@ -229,6 +230,7 @@ def create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
         report['eddy_report'] = f.readlines()
 
     report['eddy_params'] = np.genfromtxt(eddy_rms).tolist()
-
+    eddy_qc = load_json(eddy_qc_file)
+    report['eddy_quad'] = eddy_qc
     save_json(outpath, report)
     return outpath

dmriprep/run.py

@@ -752,23 +752,26 @@ def binarize_aparc(aparc_aseg):
     wf.connect(reslice_orig_to_dwi, 'out_file', datasink, 'dmriprep.anat.@T1w')
 
     def report_fn(dwi_corrected_file, eddy_rms, eddy_report,
-                  color_fa_file, anat_mask_file, outlier_indices):
+                  color_fa_file, anat_mask_file, outlier_indices,
+                  eddy_qc_file):
         from dmriprep.qc import create_report_json
 
         report = create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
-                                    color_fa_file, anat_mask_file, outlier_indices)
+                                    color_fa_file, anat_mask_file, outlier_indices,
+                                    eddy_qc_file)
         return report
 
     report_node = pe.Node(niu.Function(
         input_names=['dwi_corrected_file', 'eddy_rms',
                      'eddy_report', 'color_fa_file',
-                     'anat_mask_file', 'outlier_indices'],
+                     'anat_mask_file', 'outlier_indices', 'eddy_qc_file'],
         output_names=['report'],
         function=report_fn
     ), name="reportJSON")
 
     # for the report, lets show the eddy corrected (full volume) image
     wf.connect(voltransform, "transformed_file", report_node, 'dwi_corrected_file')
+    wf.connect(eddy_quad, 'out_qc_json', report_node, 'eddy_qc_file')
 
     # add the rms movement output from eddy
     wf.connect(prep, "fsl_eddy.out_movement_rms", report_node, 'eddy_rms')

kubernetes/setup_gcp_kubernetes_dmriprep.sh

@@ -15,4 +15,4 @@ CLUSTERNAME=dmriprep
 gcloud config set compute/zone $ZONE
 
 # start the cluster!
-gcloud beta container clusters create $CLUSTERNAME --machine-type n1-highmem-4 --enable-autoscaling --max-nodes=$MAX_NODES --num-nodes 2 --cluster-version latest --node-labels dmriprep/node-purpose=core
+gcloud beta container clusters create $CLUSTERNAME --machine-type n1-highmem-4 --enable-autoscaling --max-nodes=$MAX_NODES --num-nodes 1 --cluster-version latest --node-labels dmriprep/node-purpose=core