Merge pull request #1207 from chrisfilo/fix/spm_realign

SPM realign used to omit the first volume/run

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 +1,75 @@
+import nipype.pipeline.engine as pe
+from nipype.interfaces import spm
+from nipype.interfaces import fsl
+from nipype.algorithms.misc import Gunzip
+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()
+
+
+gunzip = pe.Node(Gunzip(), name="gunzip")
+gunzip.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"
+
+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([(gunzip, stc, [("out_file", "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')])])
+
+workflow4d.run()

nipype/interfaces/spm/preprocess.py

@@ -123,9 +123,8 @@ class RealignInputSpec(SPMCommandInputSpec):
                         desc='gaussian smoothing kernel width')
     separation = traits.Range(low=0.0, field='eoptions.sep',
                               desc='sampling separation in mm')
-    register_to_mean = traits.Bool(True, field='eoptions.rtm',
-                                   mandatory=True, usedefault=True,
-                desc='Indicate whether realignment is done to the mean image')
+    register_to_mean = traits.Bool(field='eoptions.rtm',
+                                   desc='Indicate whether realignment is done to the mean image')
     weight_img = File(exists=True, field='eoptions.weight',
                       desc='filename of weighting image')
     interp = traits.Range(low=0, high=7, field='eoptions.interp',
@@ -191,9 +190,13 @@ def _format_arg(self, opt, spec, val):
         """Convert input to appropriate format for spm
         """
         if opt == 'in_files':
+            if self.inputs.jobtype == "write":
+                separate_sessions = False
+            else:
+                separate_sessions = True
             return scans_for_fnames(val,
-                                    keep4d=True,
-                                    separate_sessions=True)
+                                    keep4d=False,
+                                    separate_sessions=separate_sessions)
         return super(Realign, self)._format_arg(opt, spec, val)
 
     def _parse_inputs(self):
@@ -206,19 +209,21 @@ def _list_outputs(self):
         outputs = self._outputs().get()
         resliced_all = self.inputs.write_which[0] > 0
         resliced_mean = self.inputs.write_which[1] > 0
-        if isdefined(self.inputs.in_files):
-            outputs['realignment_parameters'] = []
-        for imgf in self.inputs.in_files:
-            if isinstance(imgf, list):
-                tmp_imgf = imgf[0]
-            else:
-                tmp_imgf = imgf
-            outputs['realignment_parameters'].append(fname_presuffix(tmp_imgf,
-                                                                     prefix='rp_',
-                                                                     suffix='.txt',
-                                                                     use_ext=False))
-            if not isinstance(imgf, list) and func_is_3d(imgf):
-                break
+        
+        if self.inputs.jobtype != "write":
+            if isdefined(self.inputs.in_files):
+                outputs['realignment_parameters'] = []
+            for imgf in self.inputs.in_files:
+                if isinstance(imgf, list):
+                    tmp_imgf = imgf[0]
+                else:
+                    tmp_imgf = imgf
+                outputs['realignment_parameters'].append(fname_presuffix(tmp_imgf,
+                                                                         prefix='rp_',
+                                                                         suffix='.txt',
+                                                                         use_ext=False))
+                if not isinstance(imgf, list) and func_is_3d(imgf):
+                    break
         if self.inputs.jobtype == "estimate":
             outputs['realigned_files'] = self.inputs.in_files
         if self.inputs.jobtype == "estimate" or self.inputs.jobtype == "estwrite":
@@ -240,18 +245,10 @@ def _list_outputs(self):
                         for i, inner_imgf in enumerate(filename_to_list(imgf)):
                             newfile = fname_presuffix(inner_imgf,
                                                       prefix=self.inputs.out_prefix)
-                            if os.path.exists(newfile):
-                                realigned_run.append(newfile)
-                                continue
-                            if (idx == 0) and (i == 0) and \
-                                    func_is_3d(inner_imgf):
-                                realigned_run.append(fname_presuffix(inner_imgf,
-                                                                     prefix=''))
+                            realigned_run.append(newfile)
                     else:
                         realigned_run = fname_presuffix(imgf,
                                                         prefix=self.inputs.out_prefix)
-                        if (idx == 0) and func_is_3d(imgf):
-                            realigned_run = fname_presuffix(imgf, prefix='')
                     outputs['realigned_files'].append(realigned_run)
         return outputs
 

nipype/interfaces/spm/tests/test_auto_Realign.py

@@ -26,8 +26,6 @@ def test_Realign_inputs():
     quality=dict(field='eoptions.quality',
     ),
     register_to_mean=dict(field='eoptions.rtm',
-    mandatory=True,
-    usedefault=True,
     ),
     separation=dict(field='eoptions.sep',
     ),