{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "0a30a029-f85b-48bd-adfe-02a318b84611",
   "metadata": {},
   "source": [
    "# Spine Registration Example \n",
    "\n",
    "The following workflow shows how to use the scripts within this directory to register a spine image with the option to supply landmark points."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "0fde6ba6-85a5-4277-a9ee-60474b91ba02",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "d17209bf-3a7e-4950-813e-75e3f4244ece",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "# fname_I = '/home/dtward/Documents/UCLA/dong/spine_registration_2025/interpolated_atlas.npz'\n",
    "# fname_L = '/home/dtward/Documents/UCLA/dong/spine_registration_2025/interpolated_atlas_labels.npz'\n",
    "# fname_J = '/home/dtward/Documents/UCLA/dong/spine_registration_2025/Spine_Reflection.npz'\n",
    "# pointsJ_file = '/qnap/Spine_Registration/spine4_image_with_reflection/Spine_4_Morphh_Central_Canal.swc'\n",
    "\n",
    "fname_I = '/nafs/dtward/spine_work/interpolated_atlas.npz'\n",
    "fname_L = '/nafs/dtward/spine_work/interpolated_atlas_labels.npz'\n",
    "fname_J = '/nafs/dtward/spine_work/Spine_Reflection.npz'\n",
    "pointsJ_file = '/nafs/dtward/spine_work/Spine_4_Morphh_Central_Canal.swc'\n",
    "\n",
    "fname_script = '/home/abenneck/Desktop/spine_registration/spine_reg_pipeline.py'\n",
    "outdir = '/home/abenneck/Desktop/spine_outputs'\n",
    "e_path = '/home/abenneck/Desktop/emlddmm'\n",
    "command_str = f'python3 {fname_script} {fname_I} {fname_L} {fname_J} {pointsJ_file} {outdir} {e_path} -niter 5 -v'\n",
    "\n",
    "if False:\n",
    "    os.system(command_str)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "30429790-b780-430c-93b6-48a3f075c2b6",
   "metadata": {},
   "outputs": [],
   "source": [
    "# import sys\n",
    "\n",
    "# sys.path.insert(0, str(Path('..', 'src').resolve()))\n",
    "# sys.path"
   ]
  }
 ],
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