Added offset

README.rst

@@ -25,7 +25,8 @@ CLI
 ***
 
 usage: roiloc [-h] -p PATH -i INPUTPATTERN [-r ROI [ROI ...]] -c CONTRAST [-b]
-              [-t TRANSFORM] [-m MARGIN [MARGIN ...]] [--mask MASK]
+              [-t TRANSFORM] [-m MARGIN [MARGIN ...]] [--rightoffset RIGHTOFFSET [RIGHTOFFSET ...]]
+              [--leftoffset LEFTOFFSET [LEFTOFFSET ...]] [--mask MASK]
               [--extracrops EXTRACROPS [EXTRACROPS ...]] [--savesteps]
 
 arguments::
@@ -52,6 +53,18 @@ arguments::
                         has to be a list of 3 integers, to control the margin
                         in the three axis (0: left/right margin, 1: post/ant
                         margin, 2: inf/sup margin). Default: [8,8,8]
+  --rightoffset RIGHTOFFSET [RIGHTOFFSET ...]
+                        Offset to add to the bounding box of the right ROI in
+                        voxels. It has to be a list of 3 integers, to control
+                        the offset in the three axis (0: from left to right,
+                        1: from post to ant, 2: from inf to sup).
+                        Default: [0,0,0]
+  --leftoffset LEFTOFFSET [LEFTOFFSET ...]
+                        Offset to add to the bounding box of the left ROI in
+                        voxels. It has to be a list of 3 integers, to control
+                        the offset in the three axis (0: from left to right,
+                        1: from post to ant, 2: from inf to sup).
+                        Default: [0,0,0]
   --mask MASK           Pattern for brain tissue mask to improve registration
                         (e.g.: `sub_*bet_mask.nii.gz`). If providing a BET
                         mask, please also pass `-b` to use a BET MNI template.

roiloc/location.py

@@ -7,12 +7,15 @@
 from rich import print
 
 
-def get_coords(x: np.ndarray, margin: list = [8, 8, 8]) -> list:
-    """Get coordinates of a given ROI, and apply a margin.
+def get_coords(x: np.ndarray,
+               margin: list = [8, 8, 8],
+               offset: list = [0, 0, 0]) -> list:
+    """Get coordinates of a given ROI, and apply a margin with offset.
 
     Args:
         x (np.ndarray): ROI in binary format
         margin (list, optional): margin for xyz axes. Defaults to [8, 8, 8]
+        offset (list, optional): offset for xyz axes. Defaults to [0, 0, 0]
 
     Returns:
         list: Coordinates in xyzxyz format
@@ -21,9 +24,12 @@ def get_coords(x: np.ndarray, margin: list = [8, 8, 8]) -> list:
 
     mask = np.where(x != 0)
 
-    minx, maxx = int(np.min(mask[0])), int(np.max(mask[0]))
-    miny, maxy = int(np.min(mask[1])), int(np.max(mask[1]))
-    minz, maxz = int(np.min(mask[2])), int(np.max(mask[2]))
+    minx, maxx = int(np.min(mask[0])) + offset[0], int(np.max(
+        mask[0])) + offset[0]
+    miny, maxy = int(np.min(mask[1])) + offset[1], int(np.max(
+        mask[1])) + offset[1]
+    minz, maxz = int(np.min(mask[2])) + offset[2], int(np.max(
+        mask[2])) + offset[2]
 
     minx = (minx - margin[0]) if (minx - margin[0]) > 0 else 0
     miny = (miny - margin[1]) if (miny - margin[1]) > 0 else 0

roiloc/locator.py

@@ -18,7 +18,9 @@ class RoiLocator:
         bet (bool, optional): Use brain extracted MNI template. Defaults to False.
         transform_type (str, optional): Type of transformation for the registration.
                                         Defaults to "AffineFast".
-        margin (list, optional): Margin to apply. Defaults to [4, 4, 4].
+        margin (list, optional): Margin to apply. Defaults to [8, 8, 8].
+        rightoffset (list, optional): Offset to apply to the right hippocampus. Defaults to [0, 0, 0].
+        leftoffset (list, optional): Offset to apply to the left hippocampus. Defaults to [0, 0, 0].
         mask (Optional[ANTsImage], optional): Brain mask to improve registration quality.
                                               Defaults to None.
 
@@ -40,11 +42,15 @@ def __init__(self,
                  roi: str,
                  bet: bool = False,
                  transform_type: str = "AffineFast",
-                 margin: list = [4, 4, 4],
+                 margin: list = [8, 8, 8],
+                 rightoffset: list = [0, 0, 0],
+                 leftoffset: list = [0, 0, 0],
                  mask: Optional[ANTsImage] = None):
 
         self.transform_type = transform_type
         self.margin = margin
+        self.rightoffset = rightoffset
+        self.leftoffset = leftoffset
         self.mask = mask
 
         self._roi_idx = get_roi_indices(roi)
@@ -90,7 +96,10 @@ def fit(self, image: ANTsImage):
             region = get_roi(registered_atlas=registered_atlas,
                              idx=int(self._roi_idx[i]),
                              save=False)
-            coords = get_coords(region.numpy(), margin=self.margin)
+            offset = self.rightoffset if side == "right" else self.leftoffset
+            coords = get_coords(region.numpy(),
+                                margin=self.margin,
+                                offset=offset)
 
             self.coords[side] = coords
 

roiloc/roiloc.py

@@ -89,7 +89,10 @@ def main(args):
                     f"{image_stem}_{roi}_{side}_{args.transform}_mask.nii.gz",
                     save=args.savesteps)
 
-                coords = get_coords(region.numpy(), margin=args.margin)
+                offset = args.rightoffset if side == "right" else args.leftoffset
+                coords = get_coords(region.numpy(),
+                                    margin=args.margin,
+                                    offset=offset)
 
                 for file in files:
                     fstem = file.stem.split(".")[0]
@@ -167,6 +170,24 @@ def start():
         required=False,
         default=[8, 8, 8])
 
+    parser.add_argument(
+        "--rightoffset",
+        nargs='+',
+        type=int,
+        help=
+        "Offset to add to the bounding box of the right ROI in voxels. It has to be a list of 3 integers, to control the offset in the three axis (0: voxels from left to right, 1: voxels from post to ant, 2: voxels from inf to sup). Default: [0,0,0]",
+        required=False,
+        default=[0, 0, 0])
+
+    parser.add_argument(
+        "--leftoffset",
+        nargs='+',
+        type=int,
+        help=
+        "Offset to add to the bounding box of the left ROI in voxels. It has to be a list of 3 integers, to control the offset in the three axis (0: voxels from left to right, 1: voxels from post to ant, 2: voxels from inf to sup). Default: [0,0,0]",
+        required=False,
+        default=[0, 0, 0])
+
     parser.add_argument(
         "--mask",
         help=