Merge branch 'fsl_model'

Author: chrisgorgo

CHANGES

@@ -1,6 +1,6 @@
 Next release
 ============
-* ENH: New interfaces: nipy.Trim
+* ENH: New interfaces: nipy.Trim, fsl.GLM, fsl.SigLoss
 
 * ENH: Allow control over terminal output for commandline interfaces
 * ENH: New workflows for dMRI and fMRI pre-processing: added motion artifact correction

nipype/interfaces/fsl/__init__.py

@@ -11,7 +11,7 @@
                          SliceTimer, SUSAN, PRELUDE, FUGUE, FIRST)
 from .model import (Level1Design, FEAT, FEATModel, FILMGLS, FEATRegister,
                     FLAMEO, ContrastMgr, MultipleRegressDesign, L2Model, SMM,
-                    MELODIC, SmoothEstimate, Cluster, Randomise)
+                    MELODIC, SmoothEstimate, Cluster, Randomise, GLM)
 from .utils import (Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
                     ImageStats, FilterRegressor, Overlay, Slicer,
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,

nipype/interfaces/fsl/model.py

@@ -18,12 +18,12 @@
 
 import numpy as np
 
-from nipype.interfaces.fsl.base import (FSLCommand, FSLCommandInputSpec)
+from nipype.interfaces.fsl.base import (FSLCommand, FSLCommandInputSpec, Info)
 from nipype.interfaces.base import (load_template, File, traits, isdefined,
                                     TraitedSpec, BaseInterface, Directory,
                                     InputMultiPath, OutputMultiPath,
                                     BaseInterfaceInputSpec)
-from nipype.utils.filemanip import (list_to_filename, filename_to_list)
+from nipype.utils.filemanip import (list_to_filename, filename_to_list, split_filename)
 from nibabel import load
 
 warn = warnings.warn
@@ -1511,3 +1511,66 @@ def _list_outputs(self):
             outputs['f_corrected_p_files'] = glob(self._gen_fname(\
                 '%s_%s_corrp_fstat*.nii' % (self.inputs.base_name, prefix)))
         return outputs
+
+
+class GLMInputSpec(FSLCommandInputSpec):
+    in_file = File(
+        exists=True,mandatory=True,
+        argstr='-i %s',
+        desc='input 3d+t file',)
+    design = File(
+        exists=True, mandatory=True,
+        argstr='-d %s',
+        desc='design file or image file')
+    out_file = File(
+        genfile=True, argstr="-o %s",
+        desc="file or image output")
+    mask = File(
+        exists=True,
+        argstr='-m %s',
+        desc='mask file')
+    contrasts = File(
+        exists=True,
+        argstr='-c %s',
+        desc='t-contrasts file')
+    options = traits.String(
+        argstr='%s',
+        desc = 'fsl_glm options')
+class GLMOutputSpec(TraitedSpec):
+    out_file = File(
+        exists=True,
+        desc = 'file or image output')
+
+class GLM(FSLCommand):
+    """
+    FSL GLM: 
+
+    Example
+    -------
+    >>> import nipype.interfaces.fsl as fsl
+    >>> glm = fsl.GLM(in_file='functional.nii', design = 'maps.nii')
+    >>> glm.cmdline
+    """
+    _cmd = 'fsl_glm'
+    input_spec = GLMInputSpec
+    output_spec = GLMOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = self.inputs.out_file
+        # Generate an out_file if one is not provided
+        if not isdefined(outputs['out_file']) and isdefined(self.inputs.in_file):
+            ext = Info.output_type_to_ext(self.inputs.output_type)
+            if split_filename(self.inputs.in_file)[-1] in Info.ftypes.values():
+                ext = '.txt'
+            outputs['out_file'] = self._gen_fname(self.inputs.in_file,
+                                                  suffix='_glm',
+                                                  ext=ext)
+
+        return outputs
+
+    def _gen_filename(self, name):
+        if name in ('out_file'):
+            return self._list_outputs()[name]
+        else:
+            return None