Merge branch 'master' into fix/spm

Conflicts:
	nipype/interfaces/spm/preprocess.py

Author: chrisgorgo

nipype/interfaces/fsl/epi.py

@@ -654,26 +654,28 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['out_file'] = os.path.join(os.getcwd(),
                                     self.inputs.out_base + '.nii.gz')
-        outputs['out_1vol'] = os.path.join(os.getcwd(),
+        if not (isdefined(self.inputs.no_fmapreg) and self.inputs.no_fmapreg) and isdefined(self.inputs.fmap):
+            outputs['out_1vol'] = os.path.join(os.getcwd(),
                                     self.inputs.out_base + '_1vol.nii.gz')
-        outputs['fmap2str_mat'] = os.path.join(os.getcwd(),
-                                    self.inputs.out_base + '_fieldmap2str.mat')
-        outputs['fmap2epi_mat'] = os.path.join(os.getcwd(),
-                                    self.inputs.out_base + '_fieldmaprads2epi.mat')
-        outputs['fmap_epi'] = os.path.join(os.getcwd(),
-                                    self.inputs.out_base + '_fieldmaprads2epi.nii.gz')
-        outputs['fmap_str'] = os.path.join(os.getcwd(),
-                                    self.inputs.out_base + '_fieldmaprads2str.nii.gz')
-        outputs['fmapmag_str'] = os.path.join(os.getcwd(),
-                                    self.inputs.out_base + '_fieldmap2str.nii.gz')
-        outputs['epi2str_inv'] = os.path.join(os.getcwd(),
+            outputs['fmap2str_mat'] = os.path.join(os.getcwd(),
+                                        self.inputs.out_base + '_fieldmap2str.mat')
+            outputs['fmap2epi_mat'] = os.path.join(os.getcwd(),
+                                        self.inputs.out_base + '_fieldmaprads2epi.mat')
+            outputs['fmap_epi'] = os.path.join(os.getcwd(),
+                                        self.inputs.out_base + '_fieldmaprads2epi.nii.gz')
+            outputs['fmap_str'] = os.path.join(os.getcwd(),
+                                        self.inputs.out_base + '_fieldmaprads2str.ni    `i.gz')
+            outputs['fmapmag_str'] = os.path.join(os.getcwd(),
+                                        self.inputs.out_base + '_fieldmap2str.nii.gz')
+            outputs['shiftmap'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz')
+            outputs['fullwarp'] = os.path.join(os.getcwd(),
+                                    self.inputs.out_base + '_warp.nii.gz')
+            outputs['epi2str_inv'] = os.path.join(os.getcwd(),
                                     self.inputs.out_base + '_inv.mat')
+
         outputs['epi2str_mat'] = os.path.join(os.getcwd(),
                                     self.inputs.out_base + '.mat')
-        outputs['shiftmap'] = os.path.join(os.getcwd(),
-                                    self.inputs.out_base + '_fieldmaprads2epi_shift.nii.gz')
-        outputs['fullwarp'] = os.path.join(os.getcwd(),
-                                    self.inputs.out_base + '_warp.nii.gz')
         outputs['wmedge'] = os.path.join(os.getcwd(),
                                     self.inputs.out_base + '_fast_wmedge.nii.gz')
         outputs['wmseg'] = os.path.join(os.getcwd(),

nipype/interfaces/spm/preprocess.py

@@ -765,19 +765,18 @@ class Segment(SPMCommand):
     >>> seg.run() # doctest: +SKIP
 
     """
-    
 
     input_spec = SegmentInputSpec
     output_spec = SegmentOutputSpec
 
     def __init__(self, **inputs):
-        version = Info.version()
-        if version and version['name'] == "SPM12":
-            self._jobtype = 'tools'
-            self._jobname = 'oldseg'
+        _local_version = SPMCommand().version
+        if _local_version and '12.' in _local_version:
+            _jobtype = 'tools'
+            _jobname = 'oldseg'
         else:
-            self._jobtype = 'spatial'
-            self._jobname = 'preproc'
+            _jobtype = 'spatial'
+            _jobname = 'preproc'
 
         SPMCommand.__init__(self, **inputs)
 
@@ -900,13 +899,13 @@ class NewSegment(SPMCommand):
     output_spec = NewSegmentOutputSpec
 
     def __init__(self, **inputs):
-        version = Info.version()
-        if version and version['name'] == "SPM12":
-            self._jobtype = 'spatial'
-            self._jobname = 'preproc'
+        _local_version = SPMCommand().version
+        if _local_version and '12.' in _local_version:
+            _jobtype = 'spatial'
+            _jobname = 'preproc'
         else:
-            self._jobtype = 'tools'
-            self._jobname = 'preproc8'
+            _jobtype = 'tools'
+            _jobname = 'preproc8'
 
         SPMCommand.__init__(self, **inputs)
 

nipype/interfaces/spm/utils.py

@@ -450,5 +450,14 @@ def _list_outputs(self):
         from glob import glob
         outputs = self._outputs().get()
         od = os.path.abspath(self.inputs.output_dir)
-        outputs['out_files'] = glob(os.path.join(od, '*'))
+
+        ext = self.inputs.format
+        if self.inputs.output_dir_struct == "flat":
+            outputs['out_files'] = glob(os.path.join(od, '*.%s'%ext))
+        elif self.inputs.output_dir_struct == 'series':
+            outputs['out_files'] = glob(os.path.join(od, os.path.join('*','*.%s'%ext)))
+        elif self.inputs.output_dir_struct in ['patid', 'date_time', 'patname']:
+            outputs['out_files'] = glob(os.path.join(od, os.path.join('*','*','*.%s'%ext)))
+        elif self.inputs.output_dir_struct == 'patid_date':
+            outputs['out_files'] = glob(os.path.join(od, os.path.join('*','*','*','*.%s'%ext)))
         return outputs

nipype/pipeline/utils.py

@@ -993,7 +993,7 @@ def clean_working_directory(outputs, cwd, inputs, needed_outputs, config,
         inputdict = inputs.get()
         input_files.extend(walk_outputs(inputdict))
         needed_files += [path for path, type in input_files if type == 'f']
-    for extra in ['_0x*.json', 'provenance.*', 'pyscript*.m',
+    for extra in ['_0x*.json', 'provenance.*', 'pyscript*.m', 'pyjobs*.mat',
                   'command.txt', 'result*.pklz', '_inputs.pklz', '_node.pklz']:
         needed_files.extend(glob(os.path.join(cwd, extra)))
     if files2keep:

nipype/testing/data/pyscript.m

@@ -1,6 +1,14 @@
 fprintf(1,'Executing %s at %s:\n',mfilename,datestr(now));
 ver,
-try,a=1;
+try,
+if isempty(which('spm')),
+throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
+end;
+spm_path = spm('dir');
+[name, version] = spm('ver');
+fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version);
+exit;
+        
 ,catch ME,
 fprintf(2,'MATLAB code threw an exception:\n');
 fprintf(2,'%s\n',ME.message);