deploy: c428c58

Author: oesteban

_images/084cb3e03e64cec2c5a57453bfc672ccda32d24bfb311add02f08196c00cd842.png

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "45699bb0",
+   "id": "b4785e6b",
    "metadata": {},
    "source": [
     "# The extra mile\n",
@@ -16,7 +16,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "066b379e",
+   "id": "066f3029",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9b723296",
+   "id": "99b65361",
    "metadata": {},
    "source": [
     "First, use the `load()` function to create a NiBabel image object from a NIfTI file.\n",
@@ -35,7 +35,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "234480c7",
+   "id": "8ced4eac",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5998cc6a",
+   "id": "ba887b58",
    "metadata": {},
    "source": [
     "Loading in a NIfTI file with `NiBabel` gives us a special type of data object which encodes all the information in the file.\n",
@@ -60,7 +60,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "994871f2",
+   "id": "4796085c",
    "metadata": {},
    "outputs": [
     {
@@ -121,7 +121,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0aa6f2cc",
+   "id": "6b606a6a",
    "metadata": {},
    "source": [
     "### 2. Data\n",
@@ -134,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "0917d0e8",
+   "id": "bd6fb9f1",
    "metadata": {
     "tags": [
      "output_scroll"
@@ -465,7 +465,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d96aaa72",
+   "id": "dd4bbd31",
    "metadata": {},
    "source": [
     "What type of data is this exactly? We can determine this by calling the `type()` function on `dwi_data`."
@@ -474,7 +474,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "id": "6e23a551",
+   "id": "514617cf",
    "metadata": {},
    "outputs": [
     {
@@ -494,7 +494,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a651d0a0",
+   "id": "4ef25796",
    "metadata": {},
    "source": [
     "The data is a multidimensional **array** representing the image data.\n",
@@ -505,7 +505,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "a704429f",
+   "id": "044a7a47",
    "metadata": {},
    "outputs": [
     {
@@ -525,7 +525,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a31d670c",
+   "id": "0b941599",
    "metadata": {},
    "source": [
     "As expected, the data contains 4 dimensions (*i, j, k* and gradient number).\n",
@@ -536,7 +536,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "id": "175d7e3b",
+   "id": "affa31cc",
    "metadata": {},
    "outputs": [
     {
@@ -556,7 +556,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ef4100d7",
+   "id": "2b537736",
    "metadata": {},
    "source": [
     "This tells us that the image is 128, 128, 66\n",
@@ -567,7 +567,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "fcea8d80",
+   "id": "e3d01d98",
    "metadata": {
     "tags": [
      "output_scroll"
@@ -689,7 +689,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a4f6d500",
+   "id": "74a5fcae",
    "metadata": {},
    "source": [
     "### 3. [Affine](https://nipy.org/nibabel/coordinate_systems.html): tells the position of the image array data in a reference space\n",
@@ -701,7 +701,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "id": "62e9859d",
+   "id": "0d7a7633",
    "metadata": {},
    "outputs": [
     {
@@ -725,7 +725,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9eed4835",
+   "id": "6847870c",
    "metadata": {},
    "source": [
     "To explain this concept, recall that we referred to coordinates in our data as *voxel coordinates (i,j,k)* coordinates such that:\n",

_images/26bfc38d43190fd3d4fb5eccf4b695923634a1bfd02f17afa9c9caa057578dea.png

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "07c0e96c",
+   "id": "41f638b5",
    "metadata": {},
    "source": [
     "# The problem of head-motion in dMRI"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "045bf720",
+   "id": "c48d22ad",
    "metadata": {
     "tags": [
      "remove-cell"
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1e062d91",
+   "id": "0b4fe167",
    "metadata": {},
    "source": [
     "A recurring problem for any MRI acquisition is that image reconstruction and modeling are extremely sensitive to very small changes in the position of the imaged object.\n",
@@ -41,20 +41,20 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "53de77d7",
+   "id": "607ba45b",
    "metadata": {
     "tags": [
      "remove-input"
     ]
    },
    "outputs": [],
    "source": [
-    "HTML(\"\"\"<video width=\"640\" height=\"680\" loop=\"yes\" muted=\"yes\" autoplay=\"yes\" controls=\"yes\"><source src=\"../assets/videos/hm-sagittal.mp4\" type=\"video/mp4\"/></video>\"\"\")"
+    "HTML(\"\"\"<video width=\"640\" height=\"680\" loop=\"yes\" muted=\"yes\" autoplay=\"yes\" controls=\"yes\"><source src=\"../videos/hm-sagittal.mp4\" type=\"video/mp4\"/></video>\"\"\")"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "4e5c553c",
+   "id": "28cc163f",
    "metadata": {},
    "source": [
     "## Dimensions of the head-motion problem\n",
@@ -145,36 +145,16 @@
     "* A reliable registration framework to estimate the misalignment.\n",
     "* The integration of the three elements above in an iterable loop."
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "fd4f6138-709b-4368-b1f6-69123edcaf13",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "jupytext": {
-   "default_lexer": "python"
+   "default_lexer": "ipython3"
   },
   "kernelspec": {
    "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.13"
   }
  },
  "nbformat": 4,