Merge pull request #48 from richford/wnavnorm

Use WNavNorm dir from Site-CBIC

Author: akeshavan

dmriprep/__init__.py

@@ -9,6 +9,12 @@
 import errno
 import logging
 import os
+import warnings
+
+# Filter warnings that are visible whenever you import another package that
+# was compiled against an older numpy than is installed.
+warnings.filterwarnings("ignore", message="numpy.dtype size changed")
+warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
 
 from . import data
 from . import io

dmriprep/data.py

@@ -252,6 +252,16 @@ def list_all_subjects(self):
         """
         raise NotImplementedError
 
+    def filter_keys(self, subject):
+        """Study-specific S3 key filtering
+
+        Parameters
+        ----------
+        subject : dmriprep.data.Subject
+            subject instance
+        """
+        raise NotImplementedError
+
     def postprocess(self, subject):
         """Study-specific postprocessing steps
 
@@ -363,6 +373,34 @@ def get_subs_from_tsv_key(s3_key):
 
         return all_subjects
 
+    def filter_keys(self, subject):
+        """Filter S3 keys based on HBN specific vagaries
+
+        HBN Site-CBIC has multiple anatomy folders due to
+        motion correction software at the scanner level.
+        If subject.site == "Site-CBIC" then choose only the
+        anatomy files in the T1W_VNavNorm files
+
+        Parameters
+        ----------
+        subject : dmriprep.data.Subject
+            subject instance
+        """
+        if subject.site == "Site-CBIC":
+            t1w_keys = subject.s3_keys['t1w']
+            freesurfer_keys = subject.s3_keys['freesurfer']
+            correct_dir = "T1w_VNavNorm"
+
+            subject._s3_keys['t1w'] = list(filter(
+                lambda x: correct_dir in x,
+                t1w_keys
+            ))
+
+            subject._s3_keys['freesurfer'] = list(filter(
+                lambda x: correct_dir in x,
+                freesurfer_keys
+            ))
+
     def postprocess(self, subject):
         """Move the T1 file back into the freesurfer directory.
 
@@ -417,6 +455,7 @@ def __init__(self, subject_id, study, site=None):
         self._valid = False
         self._organize_s3_keys()
         if self.valid:
+            self.study.filter_keys(self)
             self._s3_keys = self._determine_directions(self._s3_keys)
             self._files = None
 

dmriprep/qc.py

@@ -10,7 +10,6 @@
 import matplotlib.pyplot as plt
 
 
-
 def reorient_array(data, aff):
     # rearrange the matrix to RAS orientation
     orientation = nib.orientations.io_orientation(aff)

dmriprep/run.py

@@ -1,11 +1,5 @@
 import os.path as op
 from shutil import copyfile
-import warnings
-
-# Filter warnings that are visible whenever you import another package that
-# was compiled against an older numpy than is installed.
-warnings.filterwarnings("ignore", message="numpy.dtype size changed")
-warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
 
 
 def run_dmriprep(dwi_file, bvec_file, bval_file,