update petsurfer.py

Author: avneetreen

nipype/interfaces/freesurfer/petsurfer.py

@@ -53,7 +53,7 @@ class GTMSegInputSpec(FSTraitedSpec):
         desc="run xcerebralseg on this subject to create apas+head.mgz"
     )
 
-    out_file = File(
+    gtm_file = File(
         argstr="--o %s",
         desc="output volume relative to subject/mri (default is gtmseg.mgz)"
     )
@@ -445,8 +445,7 @@ def _format_arg(self, name, spec, value):
 class MRTMInputSpec(GLMFitInputSpec):
 
     mrtm1 = InputMultiPath(
-        (File(exists=True, mandatory=True), 
-        File(exists=True, mandatory=True)),
+        traits.Tuple(File(exists=True, mandatory=True), File(exists=True, mandatory=True)),
         argstr="--mrtm1 %s %s...",
         desc="RefTac TimeSec : perform MRTM1 kinetic modeling",
     )
@@ -461,7 +460,7 @@ class MRTM(GLMFit):
     --------
     >>> mrtm = MRTM()
     >>> mrtm.inputs.in_file = 'tac.nii'
-    >>> gtmseg.inputs.mrtm = [('ref_tac.dat', 'timing.dat')]
+    >>> mrtm.inputs.mrtm1 = [('ref_tac.dat', 'timing.dat')]
     >>> mrtm.inputs.glmdir = 'mrtm'
     >>> mrtm.cmdline == 'mri_glmfit --glmdir mrtm --y tac.nii --mrtm1 ref_tac.dat timing.dat'
     """
@@ -502,11 +501,11 @@ class MRTM2(GLMFit):
     """Perform MRTM2 kinetic modeling.
     Examples
     --------
-    >>> mrtm = MRTM()
-    >>> mrtm.inputs.in_file = 'tac.nii'
-    >>> gtmseg.inputs.mrtm = [('ref_tac.dat', 'timing.dat', 'k2prime.dat')]
-    >>> mrtm.inputs.glmdir = 'mrtm2'
-    >>> mrtm2.cmdline == 'mri_glmfit --glmdir mrtm2 --y tac.nii --mrtm2 ref_tac.dat timing.dat k2prime.dat'
+    >>> mrtm2 = MRTM2()
+    >>> mrtm2.inputs.in_file = 'tac.nii'
+    >>> mrtm2.inputs.mrtm2 = [('ref_tac.dat', 'timing.dat', 0.07872)]
+    >>> mrtm2.inputs.glmdir = 'mrtm2'
+    >>> mrtm2.cmdline == 'mri_glmfit --glmdir mrtm2 --y tac.nii --mrtm2 ref_tac.dat timing.dat 0.07872'
     """
 
     _cmd = "mri_glmfit"
@@ -521,7 +520,7 @@ def _list_outputs(self):
             ext = '.nii'
         else:
             ext = '.mgh'            
-        outputs['bp'] = os.path.join(self.inputs.glm_dir, 'bp', ext)
+        outputs['bp'] = os.join(self.inputs.glm_dir, 'bp',  ext)
         return outputs
 
 class LoganRefInputSpec(GLMFitInputSpec):
@@ -560,5 +559,5 @@ def _list_outputs(self):
             ext = '.nii'
         else:
             ext = '.mgh'            
-        outputs['bp'] = os.path.join(self.inputs.glm_dir, 'bp' + ext)
+        outputs['bp'] = os.join(self.inputs.glm_dir, 'bp',  ext)
         return outputs