deploy: 35185e2

Author: oesteban

_sources/extra/nifti.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "f2fd87c7",
+   "id": "dcbee672",
    "metadata": {},
    "source": [
     "# The extra mile\n",
@@ -16,7 +16,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "f0d463a7",
+   "id": "bfb88a24",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b6c44014",
+   "id": "b6d4c34c",
    "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": "aae19e81",
+   "id": "2a054276",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ce26821f",
+   "id": "d9efe7bf",
    "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": "e4343aad",
+   "id": "17ab1283",
    "metadata": {},
    "outputs": [
     {
@@ -121,7 +121,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ed209848",
+   "id": "27b6f80c",
    "metadata": {},
    "source": [
     "### 2. Data\n",
@@ -134,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "4970e36a",
+   "id": "e53d29b4",
    "metadata": {
     "tags": [
      "output_scroll"
@@ -465,7 +465,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c25f90ba",
+   "id": "afe8693d",
    "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": "9a4bcefc",
+   "id": "36a36467",
    "metadata": {},
    "outputs": [
     {
@@ -494,7 +494,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "905273e9",
+   "id": "1408ff57",
    "metadata": {},
    "source": [
     "The data is a multidimensional **array** representing the image data.\n",
@@ -505,7 +505,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "bfe44b8e",
+   "id": "19b9ec12",
    "metadata": {},
    "outputs": [
     {
@@ -525,7 +525,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "4d7f56ef",
+   "id": "1e0d7624",
    "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": "64d75122",
+   "id": "26de529a",
    "metadata": {},
    "outputs": [
     {
@@ -556,7 +556,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d29ce741",
+   "id": "92bb2d1f",
    "metadata": {},
    "source": [
     "This tells us that the image is 128, 128, 66\n",
@@ -567,7 +567,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "35c88f90",
+   "id": "21539086",
    "metadata": {
     "tags": [
      "output_scroll"
@@ -689,7 +689,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ceee1f52",
+   "id": "4df216af",
    "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": "12e0203c",
+   "id": "3a939f9d",
    "metadata": {},
    "outputs": [
     {
@@ -725,7 +725,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d8692337",
+   "id": "8431c61b",
    "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",