deploy: 95d9793

Author: oesteban

_sources/extra/nifti.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "bd8e1b60",
+   "id": "ce6097b2",
    "metadata": {},
    "source": [
     "# The extra mile\n",
@@ -16,7 +16,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "625c23dc",
+   "id": "90b0175a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1ccbd3fc",
+   "id": "dbef1562",
    "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": "5774ecdf",
+   "id": "9971ef59",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5f1112c4",
+   "id": "e26439e2",
    "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": "2fe282e7",
+   "id": "a3466a05",
    "metadata": {},
    "outputs": [
     {
@@ -121,7 +121,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9e93bdcc",
+   "id": "ad0508e9",
    "metadata": {},
    "source": [
     "### 2. Data\n",
@@ -134,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "c48586f4",
+   "id": "240e9036",
    "metadata": {
     "tags": [
      "output_scroll"
@@ -465,7 +465,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c45e8656",
+   "id": "630848f9",
    "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": "569073ed",
+   "id": "a6a797e9",
    "metadata": {},
    "outputs": [
     {
@@ -494,7 +494,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f888ec95",
+   "id": "5bfd50cf",
    "metadata": {},
    "source": [
     "The data is a multidimensional **array** representing the image data.\n",
@@ -505,7 +505,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "b4181d45",
+   "id": "34cc9025",
    "metadata": {},
    "outputs": [
     {
@@ -525,7 +525,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8157e259",
+   "id": "9db12d58",
    "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": "a4cafe5e",
+   "id": "b9e46551",
    "metadata": {},
    "outputs": [
     {
@@ -556,7 +556,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2d29d8dc",
+   "id": "4f8cd3f4",
    "metadata": {},
    "source": [
     "This tells us that the image is 128, 128, 66\n",
@@ -567,7 +567,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "f798998d",
+   "id": "65a88fb3",
    "metadata": {
     "tags": [
      "output_scroll"
@@ -689,7 +689,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0e37b08a",
+   "id": "8d746ac6",
    "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": "578c4ba5",
+   "id": "c26f565e",
    "metadata": {},
    "outputs": [
     {
@@ -725,7 +725,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "66451ad0",
+   "id": "782220c2",
    "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",

_sources/notebook/01-intro.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "41f638b5",
+   "id": "9066ad1b",
    "metadata": {},
    "source": [
     "# The problem of head-motion in dMRI"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c48d22ad",
+   "id": "643d1a35",
    "metadata": {
     "tags": [
      "remove-cell"
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0b4fe167",
+   "id": "7c54063f",
    "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",
@@ -41,7 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "607ba45b",
+   "id": "3f9fa97c",
    "metadata": {
     "tags": [
      "remove-input"
@@ -54,7 +54,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "28cc163f",
+   "id": "b501d112",
    "metadata": {},
    "source": [
     "## Dimensions of the head-motion problem\n",