SPM12 outputs .nii instead of .img/.hdr

Author: chrisgorgo

examples/fmri_spm.py

@@ -18,14 +18,13 @@
 import os                                    # system functions
 
 from nipype import config
-config.enable_provenance()
+#config.enable_provenance()
 
 from nipype.interfaces import spm, fsl
 
 # In order to use this example with SPM's matlab common runtime
-# matlab_cmd = ('/Users/satra/Downloads/spm8/run_spm8.sh '
-#               '/Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ script')
-# spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+matlab_cmd = ('/Applications/spm12/run_spm12.sh /Applications/MATLAB/MATLAB_Compiler_Runtime/v713/ script')
+spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
 
 import nipype.interfaces.io as nio           # Data i/o
 import nipype.interfaces.utility as util     # utility
@@ -349,7 +348,8 @@ 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')