Added midmat argument, made some small modifications in argument description

Author: juhuntenburg

nipype/interfaces/fsl/utils.py

@@ -1575,23 +1575,26 @@ class ConvertWarpInputSpec(FSLCommandInputSpec):
  desc='filename for pre-transform (affine matrix)')
 
  warp1 = File(exists=True, argstr='--warp1=%s',
- desc=('Name of file containing warp-fields/coefficients. This could e.g. be a '
+ desc=('Name of file containing inital warp-fields/coefficients (follows premat). This could e.g. be a '
  'fnirt-transform from a subjects structural scan to an average of a group '
  'of subjects.'))
+ 
+ midmat=File(exists=True, argstr="--midmat=%s", 
+ desc="Name of file containing mid-warp-affine transform")
 
  warp2 = File(exists=True, argstr='--warp2=%s',
- desc=('Name of file containing warp-fields/coefficients. This could e.g. be a '
+ desc=('Name of file containing secondary warp-fields/coefficients (after warp1/midmat but before postmat). This could e.g. be a '
  'fnirt-transform from the average of a group of subjects to some standard '
  'space (e.g. MNI152).'))
 
  postmat = File(exists=True, argstr='--postmat=%s',
- desc=('Name of file containing an affine transform. It could e.g. be an affine '
+ desc=('Name of file containing an affine transform (applied last). It could e.g. be an affine '
  'transform that maps the MNI152-space into a better approximation to the '
  'Talairach-space (if indeed there is one).'))
 
  shift_in_file = File(exists=True, argstr='--shiftmap=%s',
  desc=('Name of file containing a "shiftmap", a non-linear transform with '
- 'displacements only in one direction. This would typically be a '
+ 'displacements only in one direction (applied first, before premat). This would typically be a '
  'fieldmap that has been pre-processed using fugue that maps a '
  'subjects functional (EPI) data onto an undistorted space (i.e. a space '
  'that corresponds to his/her true anatomy).'))
@@ -1626,12 +1629,12 @@ class ConvertWarpInputSpec(FSLCommandInputSpec):
  'coordinates in the next space.'))
 
  out_abswarp = traits.Bool(argstr='--absout', xor=['out_relwarp'],
- desc=('If set it indicates that the warps in --out should be relative, i.e. '
- 'the vaulues in --out are displacements from the coordinates in --ref.'))
+ desc=('If set it indicates that the warps in --out should be absolut, i.e. '
+ 'the values in --out are displacements from the coordinates in --ref.'))
 
  out_relwarp = traits.Bool(argstr='--relout', xor=['out_abswarp'],
  desc=('If set it indicates that the warps in --out should be relative, i.e. '
- 'the vaulues in --out are displacements from the coordinates in --ref.'))
+ 'the values in --out are displacements from the coordinates in --ref.'))
 
 
 class ConvertWarpOutputSpec(TraitedSpec):