From 06608972c7a19be09548f3a0498183ac8d9a8226 Mon Sep 17 00:00:00 2001
From: OneMore1 <129330534+OneMore1@users.noreply.github.com>
Date: Tue, 12 Nov 2024 10:01:01 +0000
Subject: [PATCH] Provide a whole-brain pre-processing process

---
 convert.ipynb | 42 ++++++++++++++++++++++++++++++++++++++----
 1 file changed, 38 insertions(+), 4 deletions(-)

diff --git a/convert.ipynb b/convert.ipynb
index cd17475..3596418 100644
--- a/convert.ipynb
+++ b/convert.ipynb
@@ -16,7 +16,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
+    "# 1. only GM, use default lfm code from https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/tdcsleadfield.html#tdcsleadfield\n",
     "f = h5py.File('hcp4_leadfield_EEG10-10_UI_Jurak_2007.hdf5','r') \n",
     "\n"
    ]
@@ -66,12 +66,46 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "# 2. for GM and WM\n",
+    "# modify the lfm code.\n",
+    "import simnibs\n",
+    "from simnibs import sim_struct\n",
+    "tdcs_lf = sim_struct.TDCSLEADFIELD()\n",
+    "tdcs_lf.fnamehead = #[your path to msh]\n",
+    "tdcs_lf.subpath = #[your path to m2m folder]\n",
+    "tdcs_lf.pathfem = #[output path]\n",
+    "tdcs_lf.interpolation = None\n",
+    "tdcs_lf.map_to_surf = False\n",
+    "tdcs_lf.tissues = [1,2]\n",
+    "simnibs.run_simnibs(tdcs_lf)\n",
+    "\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#generate lfm and pos matrix\n",
+    "f = h5py.File([your path to hdf5])\n",
+    "\n",
+    "pos = f['mesh_leadfield']['nodes']['node_coord']\n",
+    "lfm = f['mesh_leadfield']['leadfields']['tdcs_leadfield']\n",
+    "index = f['mesh_leadfield']['elm']['node_number_list']\n",
+    "newpos = np.zeros([lfm.shape[1],3])\n",
+    "for i in range(newpos.shape[0]): # The midpoint of the tetrahedron\n",
+    "    newpos[i]=(pos[index[i,0]-1]+pos[index[i,1]-1]+pos[index[i,2]-1]+pos[index[i,3]-1])/4\n",
+    "np.save('lfm_hcp4.npy',lfm)\n",
+    "np.save('pos_hcp4.npy',newpos)"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "simnibs",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -85,7 +119,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.16"
+   "version": "3.10.12"
   },
   "orig_nbformat": 4
  },