Add parcel (#317)

parcel for marmo

Author: davidmeunier79

macapype/bash/IterREGBET.sh

@@ -278,11 +278,13 @@ for ((i = 1 ; i  <= $NITER ; i++)); do
 
   # Extra whole-head non-linear registration, if wanted
   if [[ -n $REF_WHOLE ]] && [[ $i == $NITER ]]; then
-    echo "FNIRT..."
+    echo "FNIRT..." 1>&2
     "${FSLPREFIX}fnirt" --in=$IN_WHOLE --ref=$REF_WHOLE --aff=$I2R_XFM --iout=${WARP[WH_OUT]} --cout=${WARP[WH_WARP]} # compute warp
-    echo "Inverting warp..."
+    #"${FSLPREFIX}fnirt" --in=$IN_WHOLE --ref=$REF_WHOLE --aff=$I2R_XFM --iout=${WARP[WH_OUT]} --cout=${WARP[WH_WARP]} --miter=5,3 --subsamp=4,2 --infwhm=6,4 --reffwhm=4,2 --estint=false --applyrefmask=false --applyinmask=false # compute warp
+    #"${FSLPREFIX}fnirt" --in=$IN_WHOLE --ref=$REF_WHOLE --aff=$I2R_XFM --iout=${WARP[WH_OUT]} --cout=${WARP[WH_WARP]} --miter=1 --subsamp=4 --infwhm=6 --reffwhm=4 --estint=false --applyrefmask=false --applyinmask=false # compute warp
+    echo "Inverting warp..." 1>&2
     "${FSLPREFIX}invwarp" -r $IN_WHOLE -w ${WARP[WH_WARP]} -o ${WARP[WH_INVWARP]}
-    echo "Applying inverse warp..."
+    echo "Applying inverse warp..." 1>&2
     "${FSLPREFIX}applywarp" --ref=$IN_WHOLE --in=${TMP[REF_MASK]} --out=$IN_OUT_MASK --warp=${WARP[WH_INVWARP]} --interp=nn
   else
     "${FSLPREFIX}flirt" -in ${TMP[REF_MASK]} -ref $IN_WHOLE -out $IN_OUT_MASK -interp nearestneighbour -applyxfm -init $R2I_XFM # move brain mask to in_file

macapype/nodes/register.py

@@ -221,6 +221,12 @@ class IterREGBETOutputSpec(TraitedSpec):
             exists=True,
             desc="inv_transfo_file")
 
+    nonlin_warp_file = File(
+            desc="nonlin_warp_file")
+
+    nonlin_invwarp_file = File(
+            desc="nonlin_invwarp_file")
+
 
 class IterREGBET(CommandLine):
     """
@@ -334,8 +340,16 @@ def _list_outputs(self):
             outfile = self._gen_outfilename()
 
         outputs["warp_file"] = os.path.abspath(outfile + ".nii.gz")
+
         outputs["transfo_file"] = os.path.abspath(outfile + ".xfm")
         outputs["inv_transfo_file"] = os.path.abspath(outfile + "_inverse.xfm")
+
+        if isdefined(self.inputs.refw_file) and self.inputs.k is True:
+            outputs["nonlin_warp_file"] = \
+                os.path.abspath(outfile + "_Warp.nii.gz")
+            outputs["nonlin_invwarp_file"] = \
+                os.path.abspath(outfile + "_InverseWarp.nii.gz")
+
         return outputs
 
 

macapype/nodes/segment.py

@@ -248,15 +248,16 @@ def merge_imgs(list_img_files):
             path, fname, ext = split_f(img_file)
             img = nib.load(img_file)
             img_data = img.get_fdata()
-            new_img_data = np.zeros(shape=img_data.shape)
-            new_img_data[img_data != 0] += img_data[img_data != 0]
+            new_img_data = np.zeros(shape=img_data.shape, dtype=np.int32)
+            new_img_data[img_data != 0] = 1
 
         else:
             img_data = nib.load(img_file).get_fdata()
+
             assert img_data.shape == new_img_data.shape, \
                 "Error, shapes {} != {}".format(img_data.shape,
                                                 new_img_data.shape)
-            new_img_data[img_data != 0] += img_data[img_data != 0]
+            new_img_data[img_data != 0] = 1
 
     # creating indexed_mask
     merged_img = nib.Nifti1Image(dataobj=new_img_data,