added --linear option and license

Author: Ian-Goodall-Halliwell

LICENSE

@@ -0,0 +1,105 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
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+
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examples/readme.md

@@ -32,6 +32,7 @@ python synthseg_registration.py --input <input_image.nii.gz> --reference <refere
 - `--reference`: Reference/target image (any contrast)
 - `--output`: Path where the registered image will be saved
 - `--workdir`: (Optional) Directory for intermediate files (default: current directory)
+- `--linear`: (Optional) Perform linear-only registration (affine only). Skips the non-linear warping step to increase speed when deformation fields are not needed.
 
 ### Example
 

micaflow/cli.py

@@ -218,6 +218,7 @@ def print_extended_help():
       {YELLOW}--rm-cerebellum{RESET}                Remove cerebellum from brain extraction outputs
       {YELLOW}--PED{RESET}                          Phase encoding direction of DWI, options are: 'ap', 'pa', 'lr', 'rl', 'si', 'is' (default: 'pa')
       {YELLOW}--shell-dimension{RESET}              Dimension of the DWI image referring to shells (default: 3)
+      {YELLOW}--linear{RESET}                       Use linear-only registration to MNI space (faster, no nonlinear warping), default is False
       {YELLOW}Remaining arguments are passed to Snakemake for workflow management{RESET}
 
     {CYAN}{BOLD}────────────────── EXAMPLE PIPELINE USAGE ───────────────{RESET}
@@ -477,6 +478,9 @@ def format_help(self):
     pipeline_parser.add_argument(
         "--shell-dimension", type=int, default=3, help="Dimension of the DWI image referring to shells"
     )
+    pipeline_parser.add_argument(
+        "--linear", action="store_true", help="Use linear-only registration to MNI space (faster, no nonlinear warping)"
+    )
 
     # SynthSeg command
     synthseg_parser = subparsers.add_parser(
@@ -1053,6 +1057,7 @@ def format_help(self):
             "extract_brain",
             "shell_dimension",
             "PED",
+            "linear",
         ]:
             if getattr(args, param.replace("-", "_"), None):
                 config[param] = getattr(args, param.replace("-", "_"))