ENH WIP added applyxfm4d

nipype/interfaces/fsl/__init__.py

@@ -7,7 +7,7 @@
 """
 
 from .base import (FSLCommand, Info, check_fsl, no_fsl, no_fsl_course_data)
-from .preprocess import (FAST, FLIRT, ApplyXfm, BET, MCFLIRT, FNIRT, ApplyWarp,
+from .preprocess import (FAST, FLIRT, ApplyXfm, ApplyXfm4D,  BET, MCFLIRT, FNIRT, ApplyWarp,
                          SliceTimer, SUSAN, PRELUDE, FUGUE, FIRST)
 from .model import (Level1Design, FEAT, FEATModel, FILMGLS, FEATRegister,
                     FLAMEO, ContrastMgr, MultipleRegressDesign, L2Model, SMM,

nipype/interfaces/fsl/preprocess.py

@@ -592,6 +592,62 @@ class ApplyXfm(FLIRT):
     input_spec = ApplyXfmInputSpec
 
 
+class ApplyXfm4DInputSpec(FSLCommandInputSpec):
+    in_file = File(exists=True, position=0, argstr='%s', mandatory=True, desc="timeseries to motion-correct")
+    ref_vol = File(exists=True, position=1, argstr='%s', mandatory=True, desc="volume with final FOV and resolution")
+    out_file = File(exists=True, position=2, argstr='%s', genfile=True, desc="file to write", hash_files=False)
+    trans_file = File(argstr='%s', position=3, desc="single tranformation matrix", xor=["trans_dir"], requires=["single_matrix"])
+    trans_dir = File(argstr='%s', position=3, desc="folder of transformation matricies", xor=["tans_file"])
+    single_matrix = traits.Bool(argstr='-singlematrix', desc="true if applying one volume to all timepoints")
+    four_digit = traits.Bool(argstr='-fourdigit', desc="true mat names have four digits not five")
+    user_prefix = traits.Str(argstr='-userprefix %s', desc="supplied prefix if mats don't start with 'MAT_'")
+
+
+class ApplyXfm4DOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc="transform applied timeseries")
+
+class ApplyXfm4D(FSLCommand):
+    """
+    Wraps the applyxfm4D command line tool for applying one 3D transform to every volume in a 4D image OR
+    a directory of 3D tansforms to a 4D image of the same length.
+
+    Examples
+    ---------
+    >>> import nipype.interfaces.fsl as fsl
+    >>> from nipype.testing import example_data
+    >>> applyxfm4d = fsl.ApplyXfm4D()
+    >>> applyxfm4d.inputs.in_file = example_data('functional.nii')
+    >>> applyxfm4d.inputs.in_matrix_file = example_data('functional_mcf.mat')
+    >>> applyxfm4d.inputs.out_file = 'newfile.nii'
+    >>> applyxfm4d.inputs.reference = example_data('functional_mcf.nii')
+    >>> result = applyxfm.run() # doctest: +SKIP
+
+    """
+
+    _cmd = 'applyxfm4D'
+    input_spec = ApplyXfm4DInputSpec
+    output_spec = ApplyXfm4DOutputSpec
+
+    def _list_outputs(self):
+        cwd = os.getcwd()
+        outputs = self._outputs().get()
+        outputs['out_file'] = self._gen_outfilename()
+        return outputs
+
+    def _gen_filename(self, name):
+        if name == 'out_file':
+            return self._gen_outfilename()
+        return None
+
+    def _gen_outfilename(self):
+        out_file = self.inputs.out_file
+        if isdefined(out_file):
+            out_file = os.path.realpath(out_file)
+        if not isdefined(out_file) and isdefined(self.inputs.in_file):
+            out_file = self._gen_fname(self.inputs.in_file, suffix='_warp4D')
+        return os.path.abspath(out_file)
+
+
 class MCFLIRTInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, position=0, argstr="-in %s", mandatory=True,
                    desc="timeseries to motion-correct")