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nipreps · Apr 22, 2021 · ec263f4 · ec263f4
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diff --git a/_images/03-models_11_0.png b/_images/03-models_11_0.png
diff --git a/_images/03-models_13_0.png b/_images/03-models_13_0.png
diff --git a/_images/03-models_25_0.png b/_images/03-models_25_0.png
diff --git a/_images/03-models_27_0.png b/_images/03-models_27_0.png
diff --git a/_images/registration_24_0.svg b/_images/registration_24_0.svg
diff --git a/_sources/extra/nifti.ipynb b/_sources/extra/nifti.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "6ab62c4c",
+   "id": "a81c2794",
    "metadata": {},
    "source": [
     "# The extra mile\n",
@@ -16,7 +16,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "9005e4b9",
+   "id": "a1b7a08e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9933fe21",
+   "id": "7e077e7b",
    "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": "657f7d4d",
+   "id": "dc7b8062",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "38548c29",
+   "id": "0183127c",
    "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": "d9a1e3b3",
+   "id": "8a09bb27",
    "metadata": {},
    "outputs": [
     {
@@ -121,7 +121,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7ebf34d6",
+   "id": "2579083a",
    "metadata": {},
    "source": [
     "### 2. Data\n",
@@ -134,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "8e6a1e53",
+   "id": "25e64938",
    "metadata": {
     "tags": [
      "output_scroll"
@@ -465,7 +465,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8c98779d",
+   "id": "460b7b2f",
    "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": "f2d3b453",
+   "id": "4e7d2b57",
    "metadata": {},
    "outputs": [
     {
@@ -494,7 +494,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "786fc1d0",
+   "id": "1cc74f1f",
    "metadata": {},
    "source": [
     "The data is a multidimensional **array** representing the image data.\n",
@@ -505,7 +505,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "0417ff66",
+   "id": "af8e1e48",
    "metadata": {},
    "outputs": [
     {
@@ -525,7 +525,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3b5ea1ef",
+   "id": "7337aec9",
    "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": "34619214",
+   "id": "77b9f659",
    "metadata": {},
    "outputs": [
     {
@@ -556,7 +556,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "de54cb89",
+   "id": "56d0b719",
    "metadata": {},
    "source": [
     "This tells us that the image is 128, 128, 66\n",
@@ -567,7 +567,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "9feb8432",
+   "id": "21bff7f0",
    "metadata": {
     "tags": [
      "output_scroll"
@@ -737,7 +737,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "85a9480b",
+   "id": "b9687a37",
    "metadata": {},
    "source": [
     "### 3. [Affine](https://nipy.org/nibabel/coordinate_systems.html): tells the position of the image array data in a reference space\n",
@@ -749,7 +749,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "id": "3d086420",
+   "id": "f6e0601c",
    "metadata": {},
    "outputs": [
     {
@@ -773,7 +773,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b618508d",
+   "id": "9cbde29f",
    "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",