fixed several bugs. tested in practice

Author: oesteban

nipype/algorithms/misc.py

@@ -1381,7 +1381,12 @@ def merge_rois(in_files, in_idxs, in_ref,
     rsh = ref.get_shape()
     del ref
     npix = rsh[0] * rsh[1] * rsh[2]
-    ndirs = nb.load(in_files[0]).get_shape()[-1]
+    fcdata = nb.load(in_files[0]).get_data()
+
+    if fcdata.ndim == 4: 
+        ndirs = fcdata.shape[-1]
+    else:
+        ndirs = 1
     newshape = (rsh[0], rsh[1], rsh[2], ndirs)
     hdr.set_data_dtype(dtype)
     hdr.set_xyzt_units('mm', 'sec')
@@ -1394,7 +1399,12 @@ def merge_rois(in_files, in_idxs, in_ref,
             cdata = nb.load(cname).get_data().reshape(-1, ndirs)
             nels = len(idxs)
             idata = (idxs, )
-            data[idata, ...] = cdata[0:nels, ...]
+            try:
+                data[idata, ...] = cdata[0:nels, ...]
+            except:
+                print(data.shape, cdata.shape)
+                raise
+                
         hdr.set_data_shape(newshape)
 
         nb.Nifti1Image(data.reshape(newshape).astype(dtype),

nipype/interfaces/fsl/base.py

@@ -367,13 +367,15 @@ def _list_outputs(self):
         for k in multi_out:
             outputs[k] = []
 
-        for i in xrange(1, self.inputs.n_fibres + 1):
-            outputs['dyads'].append(self._gen_fname('dyads%d' % i,
-                                    cwd=out_dir))
+        for i in xrange(self.inputs.n_fibres + 1):
             outputs['fsamples'].append(self._gen_fname('f%dsamples' % i,
                                        cwd=out_dir))
             outputs['mean_fsamples'].append(self._gen_fname(('mean_f%d'
                                             'samples') % i, cwd=out_dir))
+
+        for i in xrange(1, self.inputs.n_fibres + 1):
+            outputs['dyads'].append(self._gen_fname('dyads%d' % i,
+                                    cwd=out_dir))
             outputs['phsamples'].append(self._gen_fname('ph%dsamples' % i,
                                         cwd=out_dir))
             outputs['thsamples'].append(self._gen_fname('th%dsamples' % i,