Improvements on TOPUP and related workflow

Author: oesteban

nipype/interfaces/fsl/epi.py

@@ -102,7 +102,7 @@ class TOPUPInputSpec( FSLCommandInputSpec ):
  in_file = File( exists=True, mandatory=True, desc='name of 4D file with images', argstr='--imain=%s' )
  encoding_file = File( exists=True, desc='name of text file with PE directions/times', argstr='--datain=%s' )
  encoding_direction = traits.Enum( 'y','x','z','x-','y-','z-', desc='encoding direction for automatic generation of encoding_file' )
- readout_times = traits.List( desc='readout times (dwell times by # phase-encode steps minus 1)' )
+ readout_times = traits.List(traits.Float, desc='readout times (dwell times by # phase-encode steps minus 1)' )
  out_base = File( desc='base-name of output files (spline coefficients (Hz) and movement parameters)', argstr='--out=%s' )
  out_field = File( argstr='--fout=%s', desc='name of image file with field (Hz)' )
  out_corrected = File( argstr='--iout=%s', desc='name of 4D image file with unwarped images' )
@@ -166,12 +166,13 @@ def _parse_inputs( self, skip=None ):
  skip.append( 'readout_times' )
  else:
  encdir = 'y'
- enctimes = [1.0,1.0]
+ enctimes = None
+
  if isdefined( self.inputs.encoding_direction ):
  encdir = self.inputs.encoding_direction
 
  if isdefined( self.inputs.readout_times ):
- enctimes = np.array( self.inputs.readout_times, dtype=float )
+ enctimes = self.inputs.readout_times
 
  self.inputs.encoding_file = self._generate_encfile( encdir, enctimes )
 
@@ -200,12 +201,15 @@ def _list_outputs(self):
  outputs['out_logfile'] = Undefined
  return outputs
 
- def _generate_encfile( self, encdir,enctime ):
+ def _generate_encfile( self, encdir, enctime=None ):
  out_file = '%s_encfile.txt' % self.inputs.out_base 
  direction = 1.0 
  if len(encdir)==2 and encdir[1]=='-':
  direction = -1.0
 
+ if enctime is None:
+ enctime=[ 1.0, 1.0 ]
+
  file1 = [ float(val[0]==encdir[0]) * direction for val in [ 'x', 'y', 'z' ] ]
  file2 = [ float(val[0]==encdir[0]) * direction * -1.0 for val in [ 'x', 'y', 'z' ] ]
 

nipype/workflows/dmri/fsl/epi.py

@@ -389,7 +389,7 @@ def topup_correction( name='topup_correction' ):
  fields=['in_file_dir',
  'in_file_rev',
  'encoding_direction',
- 'readout_times'
+ 'readout_times',
  'ref_num'
  ]), name='inputnode'
  )