fix: spm12b compatibility

Author: satra

CHANGES

@@ -19,6 +19,7 @@ Next Release
 * ENH: New ANTs interface: LaplacianThickness
 * FIX: MRTrix tracking algorithms were ignoring mask parameters.
 * FIX: FNIRT registration pathway and associated OpenFMRI example script
+* FIX: spm12b compatibility for Model estimate
 
 Release 0.9.2 (January 31, 2014)
 ============

examples/fmri_spm.py

@@ -15,6 +15,8 @@
 
 Import necessary modules from nipype."""
 
+import os                                    # system functions
+
 from nipype import config
 config.enable_provenance()
 
@@ -30,8 +32,7 @@
 import nipype.pipeline.engine as pe          # pypeline engine
 import nipype.algorithms.rapidart as ra      # artifact detection
 import nipype.algorithms.modelgen as model   # model specification
-import os                                    # system functions
-
+import nipype.interfaces.matlab as mlab
 """
 
 Preliminaries
@@ -50,6 +51,8 @@
 # import nipype.interfaces.matlab as mlab      # how to run matlab
 # mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodesktop -nosplash")
 
+mlab.MatlabCommand.set_default_paths('/software/matlab/spm12b/spm12b_r5918')
+
 """The nipype tutorial contains data for two subjects.  Subject data
 is in two subdirectories, ``s1`` and ``s2``.  Each subject directory
 contains four functional volumes: f3.nii, f5.nii, f7.nii, f10.nii. And
@@ -70,7 +73,7 @@
 # Specify the location of the data.
 data_dir = os.path.abspath('data')
 # Specify the subject directories
-subject_list = ['s1', 's3']
+subject_list = ['s1'] #, 's3']
 # Map field names to individual subject runs.
 info = dict(func=[['subject_id', ['f3','f5','f7','f10']]],
             struct=[['subject_id','struct']])
@@ -392,4 +395,4 @@ def getstripdir(subject_id):
 
 if __name__ == '__main__':
     l1pipeline.run('MultiProc')
-    l2pipeline.run('MultiProc')
+    #l2pipeline.run('MultiProc')

nipype/interfaces/spm/model.py

@@ -213,17 +213,27 @@ def _parse_inputs(self):
     def _list_outputs(self):
         outputs = self._outputs().get()
         pth, _ = os.path.split(self.inputs.spm_mat_file)
-        mask = os.path.join(pth, 'mask.img')
+        spm12 = '12' in self.version.split('.')[0]
+        if spm12:
+            mask = os.path.join(pth, 'mask.nii')
+        else:
+            mask = os.path.join(pth, 'mask.img')
         outputs['mask_image'] = mask
         spm = sio.loadmat(self.inputs.spm_mat_file, struct_as_record=False)
         betas = []
         for vbeta in spm['SPM'][0, 0].Vbeta[0]:
             betas.append(str(os.path.join(pth, vbeta.fname[0])))
         if betas:
             outputs['beta_images'] = betas
-        resms = os.path.join(pth, 'ResMS.img')
+        if spm12:
+            resms = os.path.join(pth, 'ResMS.nii')
+        else:
+            resms = os.path.join(pth, 'ResMS.img')
         outputs['residual_image'] = resms
-        rpv = os.path.join(pth, 'RPV.img')
+        if spm12:
+            rpv = os.path.join(pth, 'RPV.nii')
+        else:
+            rpv = os.path.join(pth, 'RPV.img')
         outputs['RPVimage'] = rpv
         spm = os.path.join(pth, 'SPM.mat')
         outputs['spm_mat_file'] = spm
@@ -382,10 +392,17 @@ def _list_outputs(self):
         if con_images:
             outputs['con_images'] = con_images
             outputs['spmT_images'] = spmT_images
-        ess = glob(os.path.join(pth, 'ess*.img'))
+        spm12 = '12' in self.version.split('.')[0]
+        if spm12:
+            ess = glob(os.path.join(pth, 'ess*.nii'))
+        else:
+            ess = glob(os.path.join(pth, 'ess*.img'))
         if len(ess) > 0:
             outputs['ess_images'] = sorted(ess)
-        spmf = glob(os.path.join(pth, 'spmF*.img'))
+        if spm12:
+            spmf = glob(os.path.join(pth, 'spmF*.nii'))
+        else:
+            spmf = glob(os.path.join(pth, 'spmF*.img'))
         if len(spmf) > 0:
             outputs['spmF_images'] = sorted(spmf)
         outputs['spm_mat_file'] = self.inputs.spm_mat_file