added test workflows

Author: chrisgorgo

circle.yml

@@ -29,6 +29,12 @@ test:
         timeout: 2600
     - set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
     - cat ~/log.txt && if grep -q "ERROR" ~/log.txt; then false; else true; fi
+    - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && python ~/nipype/tools/run_examples.py test_spm Linear workflow3d workflow4d:
+        pwd: ../examples
+        environment:
+          SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
+          FORCE_SPMMCR: 1
+        timeout: 1600
     - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && python ~/nipype/tools/run_examples.py fmri_fsl_feeds Linear l1pipeline:
         pwd: ../examples
     - . /usr/share/fsl/5.0/etc/fslconf/fsl.sh && python ~/nipype/tools/run_examples.py fmri_spm_dartel Linear level1 l2pipeline:

examples/test_spm.py

@@ -0,0 +1,71 @@
+import nipype.pipeline.engine as pe
+from nipype.interfaces import spm
+from nipype.interfaces import fsl
+import os
+
+in_file = "feeds/data/fmri.nii.gz"
+
+split = pe.Node(fsl.Split(dimension="t", output_type="NIFTI"), name="split")
+split.inputs.in_file = os.path.abspath(in_file)
+
+stc = pe.Node(interface=spm.SliceTiming(), name='stc')
+stc.inputs.num_slices = 21
+stc.inputs.time_repetition = 1.0
+stc.inputs.time_acquisition = 2. - 2./32
+stc.inputs.slice_order = range(21,0,-1) 
+stc.inputs.ref_slice = 10 
+
+realign_estimate = pe.Node(interface=spm.Realign(), name='realign_estimate')
+realign_estimate.inputs.jobtype = "estimate"
+
+realign_write = pe.Node(interface=spm.Realign(), name='realign_write')
+realign_write.inputs.jobtype = "write"
+
+realign_estwrite = pe.Node(interface=spm.Realign(), name='realign_estwrite')
+realign_estwrite.inputs.jobtype = "estwrite"
+realign_estwrite.inputs.register_to_mean = True
+
+smooth = pe.Node(interface=spm.Smooth(), name = 'smooth')
+smooth.inputs.fwhm = [6, 6, 6]
+
+workflow3d = pe.Workflow(name='test_3d')
+workflow3d.base_dir = "/tmp"
+
+workflow3d.connect([(split, stc, [("out_files", "in_files")]),
+                    (stc, realign_estimate, [('timecorrected_files','in_files')]),
+                    (realign_estimate, realign_write, [('modified_in_files','in_files')]),
+                    (stc, realign_estwrite,  [('timecorrected_files','in_files')]),
+                    (realign_write, smooth, [('realigned_files','in_files')])])
+
+workflow3d.run()
+
+
+stc = pe.Node(interface=spm.SliceTiming(), name='stc')
+stc.inputs.in_files = os.path.abspath(in_file)
+stc.inputs.num_slices = 25
+stc.inputs.time_repetition = 3.0
+stc.inputs.time_acquisition = 2. - 2./32
+stc.inputs.slice_order = range(25,0,-1) 
+stc.inputs.ref_slice = 10 
+
+realign_estimate = pe.Node(interface=spm.Realign(), name='realign_estimate')
+realign_estimate.inputs.jobtype = "estimate"
+
+realign_write = pe.Node(interface=spm.Realign(), name='realign_write')
+realign_write.inputs.jobtype = "write"
+
+realign_estwrite = pe.Node(interface=spm.Realign(), name='realign_estwrite')
+realign_estwrite.inputs.jobtype = "estwrite"
+
+smooth = pe.Node(interface=spm.Smooth(), name = 'smooth')
+smooth.inputs.fwhm = [6, 6, 6]
+
+workflow4d = pe.Workflow(name='test_4d')
+workflow4d.base_dir = "/tmp"
+
+workflow4d.connect([(stc, realign_estimate, [('timecorrected_files','in_files')]),
+                    (realign_estimate, realign_write, [('modified_in_files','in_files')]),
+                    (stc, realign_estwrite,  [('timecorrected_files','in_files')]),
+                    (realign_write, smooth, [('realigned_files','in_files')])])
+
+workflow4d.run()