Add MNI-aligned templates and --legacy flag (fixes #74)

pydeface/__main__.py

@@ -6,6 +6,7 @@
 import sys
 import warnings
 from importlib.metadata import PackageNotFoundError, version
+from importlib.resources import files
 
 import numpy as np
 from nibabel import Nifti1Image, load
@@ -86,6 +87,12 @@ def main():
         ),
     )
 
+    parser.add_argument(
+        '--legacy',
+        action='store_true',
+        help='Use the legacy non-MNI-aligned templates (default is to use MNI aligned templates)',
+    )
+
     parser.add_argument(
         '--facemask',
         metavar='path',
@@ -125,6 +132,15 @@ def main():
     if args.debug:
         setup_exceptionhook()
 
+    # set templates to legacy if option used
+    if args.legacy:
+        if args.template is None:
+            args.template = files('pydeface').joinpath(
+                'data/mean_reg2mean_legacy.nii.gz'
+            )
+        if args.facemask is None:
+            args.facemask = files('pydeface').joinpath('data/facemask_legacy.nii.gz')
+
     warped_mask_img, warped_mask, template_reg, template_reg_mat = pdu.deface_image(
         **vars(args)
     )

pydeface/data/legacy2newmean.mat

@@ -0,0 +1,4 @@
+1.108074774  0.01992879549  0.01760005874  7.690653477
+-0.03829762105  1.062082491  0.1575271117  -13.01558527
+-0.005344654755  -0.1039138197  1.103534957  33.20197035
+0  0  0  1