fix the truncation so that all fmap files get truncated

Author: danielasay

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__ = '1.6.6'
+__version__ = '1.6.7'
 __author__ = 'Neuroinformatics Research Group'
 __author_email__ = 'info@neuroinfo.org'

dwiqc/tasks/qsiprep.py

@@ -353,13 +353,23 @@ def extract_vols(self, dwi_full_path, dwi_basename):
 
 		self.insert_json_value('IntendedFor', f'ses-{self._ses}/dwi/{dwi_basename}', fmap_json_file_path)
 
-		if self._truncate_fmap:
-			shape = nib.load(fmap_path).get_fdata().shape
+
+	def execute_fmap_truncation(self)
+	"""
+	If truncate fmaps is true, this method will go through all of the fmaps in the fmap BIDS dir and make sure they are only one volume in length
+	"""
+	if self._truncate_fmap:
+		fmap_files = self._layout.get(subject=self._sub, session=self._ses, suffix='epi', extension='.nii.gz', return_type='filename')
+
+		for fmap in fmap_files:
+			shape = nib.load(fmap).get_fdata().shape
 			if len(shape) == 4:
 				num_vols = shape[3]
+				if num_vols == 1:
+					continue
 				middle_vol = num_vols // 2
 
-				self.run_fslroi(fmap_path, middle_vol)
+				self.run_fslroi(fmap, middle_vol)
 
 	def run_fslroi(self, fmap, volume):
 		vol_index = int(volume) - 1
@@ -529,6 +539,7 @@ def build(self):
 		self.check_output_resolution()
 		self.check_fieldmaps()
 		self.delete_bval_bvec()
+		self.execute_fmap_truncation()
 		try:
 			qsiprep_command = yaml.safe_load(open(self._qsiprep_config))
 		except yaml.parser.ParserError: