Merge pull request #945 from chrisfilo/fix/spm12

Fix/spm12

Author: satra

examples/fmri_spm.py

@@ -18,7 +18,7 @@
 import os                                    # system functions
 
 from nipype import config
-config.enable_provenance()
+#config.enable_provenance()
 
 from nipype.interfaces import spm, fsl
 
@@ -349,7 +349,8 @@ def getstripdir(subject_id):
 # collect all the con images for each contrast.
 contrast_ids = range(1,len(contrasts)+1)
 l2source = pe.Node(nio.DataGrabber(infields=['fwhm', 'con']), name="l2source")
-l2source.inputs.template=os.path.abspath('spm_tutorial/l1output/*/con*/*/_fwhm_%d/con_%04d.img')
+# we use .*i* to capture both .img (SPM8) and .nii (SPM12)
+l2source.inputs.template=os.path.abspath('spm_tutorial/l1output/*/con*/*/_fwhm_%d/con_%04d.*i*')
 # iterate over all contrast images
 l2source.iterables = [('fwhm',fwhmlist),
                       ('con',contrast_ids)]

examples/fmri_spm_dartel.py

@@ -481,7 +481,8 @@ def getstripdir(subject_id):
 # collect all the con images for each contrast.
 contrast_ids = range(1,len(contrasts)+1)
 l2source = pe.Node(nio.DataGrabber(infields=['fwhm', 'con']), name="l2source")
-l2source.inputs.template=os.path.abspath('spm_dartel_tutorial/l1output/*/con*/*/_fwhm_%d/con_%04d.img')
+# we use .*i* to capture both .img (SPM8) and .nii (SPM12)
+l2source.inputs.template=os.path.abspath('spm_dartel_tutorial/l1output/*/con*/*/_fwhm_%d/con_%04d.*i*')
 # iterate over all contrast images
 l2source.iterables = [('fwhm',fwhmlist),
                       ('con',contrast_ids)]

examples/fmri_spm_nested.py

@@ -419,7 +419,7 @@ def getstripdir(subject_id):
 """
 
 if __name__ == '__main__':
-    level1.run()
+    level1.run('MultiProc')
     level1.write_graph()
 
 """
@@ -435,7 +435,8 @@ def getstripdir(subject_id):
 # collect all the con images for each contrast.
 contrast_ids = range(1,len(contrasts)+1)
 l2source = pe.Node(nio.DataGrabber(infields=['fwhm', 'con']), name="l2source")
-l2source.inputs.template=os.path.abspath('spm_tutorial2/l1output/*/con*/*/_fwhm_%d/con_%04d.img')
+# we use .*i* to capture both .img (SPM8) and .nii (SPM12)
+l2source.inputs.template=os.path.abspath('spm_tutorial2/l1output/*/con*/*/_fwhm_%d/con_%04d.*i*')
 # iterate over all contrast images
 l2source.iterables = [('fwhm',fwhmlist),
                       ('con',contrast_ids)]
@@ -477,5 +478,5 @@ def getstripdir(subject_id):
 """
 
 if __name__ == '__main__':
-    l2pipeline.run()
+    l2pipeline.run('MultiProc')
 

nipype/workflows/fmri/spm/preprocess.py

@@ -254,21 +254,32 @@ def create_DARTEL_template(name='dartel_template'):
                              iterfield=['channel_files'],
                              name='segment')
     workflow.connect(inputnode, 'structural_files', segment, 'channel_files')
-    if not no_matlab:
-        version = spm.Info.version()
-        if version and version['name'] == 'SPM8':
-            spm_path = version['path']
+    
+    version = spm.Info.version()
+    if version:
+        spm_path = version['path']
+        if version['name'] == 'SPM8':          
             tissue1 = ((os.path.join(spm_path,'toolbox/Seg/TPM.nii'), 1), 2, (True,True), (False, False))
             tissue2 = ((os.path.join(spm_path,'toolbox/Seg/TPM.nii'), 2), 2, (True,True), (False, False))
             tissue3 = ((os.path.join(spm_path,'toolbox/Seg/TPM.nii'), 3), 2, (True,False), (False, False))
             tissue4 = ((os.path.join(spm_path,'toolbox/Seg/TPM.nii'), 4), 3, (False,False), (False, False))
             tissue5 = ((os.path.join(spm_path,'toolbox/Seg/TPM.nii'), 5), 4, (False,False), (False, False))
             tissue6 = ((os.path.join(spm_path,'toolbox/Seg/TPM.nii'), 6), 2, (False,False), (False, False))
-            segment.inputs.tissues = [tissue1, tissue2, tissue3, tissue4, tissue5, tissue6]
+        elif version['name'] == 'SPM12':
+            spm_path = version['path']
+            tissue1 = ((os.path.join(spm_path,'tpm/TPM.nii'), 1), 1, (True,True), (False, False))
+            tissue2 = ((os.path.join(spm_path,'tpm/TPM.nii'), 2), 1, (True,True), (False, False))
+            tissue3 = ((os.path.join(spm_path,'tpm/TPM.nii'), 3), 2, (True,False), (False, False))
+            tissue4 = ((os.path.join(spm_path,'tpm/TPM.nii'), 4), 3, (False,False), (False, False))
+            tissue5 = ((os.path.join(spm_path,'tpm/TPM.nii'), 5), 4, (False,False), (False, False))
+            tissue6 = ((os.path.join(spm_path,'tpm/TPM.nii'), 6), 2, (False,False), (False, False))
         else:
-            logger.critical('SPM8 not found: DARTEL not available')
+            logger.critical('Unsupported version of SPM')
+            
+        segment.inputs.tissues = [tissue1, tissue2, tissue3, tissue4, tissue5, tissue6]
     else:
-        logger.critical('MATLAB not found: DARTEL not setting tissue templates')
+        logger.critical('SPM not found')
+        
     dartel = pe.Node(spm.DARTEL(), name='dartel')
 
     """Get the gray and white segmentation classes generated by NewSegment