new version with truncation happening in copy_inputs method

dwiqc/__version__.py

@@ -1,6 +1,6 @@
 __title__ = 'dwiqc'
 __description__ = 'Quality Assurance Pipeline for Diffusion MR Data'
 __url__ = 'https://github.com/harvard-nrg/dwiqc'
-__version__ = '1.6.3'
+__version__ = '1.6.4'
 __author__ = 'Neuroinformatics Research Group'
 __author_email__ = 'info@neuroinfo.org'

dwiqc/tasks/prequal.py

@@ -51,28 +51,30 @@ def copy_inputs(self, inputs_dir):
 
 		all_files = self._layout.get(subject=self._sub, session=self._ses, return_type='filename') # get a list of all of the subject's files
 
+		# remove all non b0volumes from the fieldmaps. return a list of paths to newly truncated files
+
+		fmap_files = self._layout.get(subject=self._sub, session=self._ses, suffix='epi', extension='.nii.gz', return_type='filename')
+
+		if not fmap_files:
+			self._layout.get(subject=self._sub, session=self._ses, suffix='epi', extension='.nii', return_type='filename')
+
+		# truncate down the fmap files to include just b0 volumes
+
+		truncated_fmaps = self.truncate_fmaps(fmap_files, inputs_dir)
+
 		# copy the all the subject's files into the INPUTS directory
 		for file in all_files:
 			basename = os.path.basename(file)
 			dest = os.path.join(inputs_dir, basename)
 			shutil.copy(file, dest)
 
-		self.create_bfiles(inputs_dir)
+		self.create_bfiles(inputs_dir, truncated_fmaps)
 
 
 	# the fieldmap data needs accompanying 'dummy' bval and bvec files that consist of 0's
-	def create_bfiles(self, inputs_dir):
+	def create_bfiles(self, inputs_dir, truncated_fmaps):
 		# get a list of all the fmap files that end with .json (this it's helpful to have a file with just one extension)
 
-		fmap_files = self._layout.get(subject=self._sub, session=self._ses, suffix='epi', extension='.nii.gz', return_type='filename')
-
-		if not fmap_files:
-			self._layout.get(subject=self._sub, session=self._ses, suffix='epi', extension='.nii', return_type='filename')
-
-		# truncate down the fmap files to include just b0 volumes
-
-		truncated_fmaps = self.truncate_fmaps(fmap_files, inputs_dir)
-
 		# get the basename of the file and then remove the extension
 		for fmap in truncated_fmaps:
 
@@ -134,11 +136,11 @@ def truncate_fmaps(self, fmap_files, inputs_dir):
 			cmd = [
 				'singularity',
 				'exec',
-				'--pwd', inputs_dir,
+				'--pwd', fmap_dir,
 				self._fsl_sif,
 				'/APPS/fsl/bin/fslselectvols',
 				'-i', fmap_basename,
-				'-o', f'{inputs_dir}/{fmap_basename}',
+				'-o', fmap_basename,
 				'--vols=0'
 			]
 			#logger.info(f'running {json.dumps(cmd, indent=2)} on {fmap}')