Merge pull request #207 from nipreps/fix/multiple-field-apply

FIX: Make sure the VSM is not modified when accessing it

sdcflows/interfaces/bspline.py

@@ -251,8 +251,6 @@ def _run_interface(self, runtime):
             pe_dir = [pe_dir[0]] * n_inputs
 
         for fname, pe, ro in zip(self.inputs.in_target, pe_dir, ro_time):
-            xfm.fit(fname)
-
             # Generate warpfield
             warp_name = filename(fname, suffix="_xfm")
             xfm.to_displacements(ro_time=ro, pe_dir=pe).to_filename(warp_name)
@@ -443,7 +441,5 @@ def _fix_topup_fieldcoeff(in_coeff, fmap_ref, refpe_reversed=False, out_file=Non
     coeffnii.header.set_qform(coeffnii.header.get_qform(coded=False), code=0)
     coeffnii.header.set_sform(newaff, code=1)
 
-    # If the reference is reversed encoded, flip the displacements
-    coeffs = (1.0 - 2.0 * refpe_reversed) * np.asanyarray(coeffnii.dataobj)
-    coeffnii.__class__(coeffs, newaff, header).to_filename(out_file)
+    coeffnii.__class__(coeffnii.dataobj, newaff, header).to_filename(out_file)
     return out_file

sdcflows/transform.py

@@ -103,7 +103,7 @@ def apply(
         """
         # Ensure the vsm has been computed
         self.fit(spatialimage)
-        vsm = self.shifts.get_fdata()
+        vsm = self.shifts.get_fdata().copy()
 
         # Reverse shifts if reversed blips
         if pe_dir.endswith("-"):
@@ -164,7 +164,7 @@ def to_displacements(self, ro_time, pe_dir):
         from nibabel.orientations import io_orientation
 
         # Generate warp field
-        data = self.shifts.get_fdata(dtype="float32")
+        data = self.shifts.get_fdata(dtype="float32").copy()
         pe_axis = "ijk".index(pe_dir[0])
         pe_sign = -1.0 if pe_dir.endswith("-") else 1.0
         pe_size = self.shifts.header.get_zooms()[pe_axis]

sdcflows/workflows/fit/pepolar.py

@@ -128,7 +128,7 @@ def init_topup_wf(
 
     brainextraction_wf = init_brainextraction_wf()
 
-    def _getpe(in_meta):
+    def _getfirstpe(in_meta):
         if isinstance(in_meta, list):
             in_meta = in_meta[0]
         return in_meta["PhaseEncodingDirection"]
@@ -144,7 +144,7 @@ def _getpe(in_meta):
         (readout_time, topup, [("readout_time", "readout_times")]),
         (concat_blips, topup, [("out_file", "in_file")]),
         (flatten, fix_coeff, [(("out_data", _front), "fmap_ref"),
-                              (("out_meta", _getpe), "pe_dir")]),
+                              (("out_meta", _getfirstpe), "pe_dir")]),
         (topup, fix_coeff, [("out_fieldcoef", "in_coeff")]),
         (topup, outputnode, [("out_jacs", "jacobians"),
                              ("out_mats", "xfms")]),
@@ -168,6 +168,7 @@ def _getpe(in_meta):
     from ...interfaces.bspline import ApplyCoeffsField
 
     unwarp = pe.Node(ApplyCoeffsField(), name="unwarp")
+    unwarp.interface._always_run = True
 
     def _getpe(inlist):
         if isinstance(inlist, dict):