Update tutorial notebooks

Author: github-actions[bot]

docs/notebook/01-intro.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "d6586284",
+   "id": "2000f9bd",
    "metadata": {},
    "source": [
     "# The problem of head-motion in dMRI"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "866a3443",
+   "id": "16e3b7ac",
    "metadata": {
     "tags": [
      "remove-cell"
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "49b5afd6",
+   "id": "899f3c43",
    "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": "e779ac52",
+   "id": "75a8775e",
    "metadata": {
     "tags": [
      "remove-input"
@@ -54,7 +54,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5d008192",
+   "id": "bea63d55",
    "metadata": {},
    "source": [
     "## Dimensions of the head-motion problem\n",

docs/notebook/02-data.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "60b5e291",
+   "id": "5fd862f3",
    "metadata": {},
    "source": [
     "# Introduction to dMRI data"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f55c036f",
+   "id": "5664b87d",
    "metadata": {
     "tags": [
      "remove-cell"
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "53e08b2f",
+   "id": "648db9eb",
    "metadata": {},
    "source": [
     "Diffusion imaging probes the random, microscopic movement of water molecules by using MRI sequences that are sensitive to the geometry and environmental organization surrounding these protons.\n",
@@ -40,7 +40,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "45f14017",
+   "id": "2eea8b8a",
    "metadata": {
     "tags": [
      "remove-input"
@@ -53,7 +53,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ca95e692",
+   "id": "116dbb36",
    "metadata": {},
    "source": [
     "*Sourced from Dr. A. Rokem, DIPY Workshop 2021*\n",
@@ -86,7 +86,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fa2291b3",
+   "id": "a07690dd",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -124,7 +124,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8cd9d100",
+   "id": "87c993b0",
    "metadata": {},
    "source": [
     "This code implements several *attributes* as well as a *behavior* - the `__len__` *method*.\n",
@@ -136,7 +136,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a0f97868",
+   "id": "ad54c224",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -152,7 +152,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "816f0374",
+   "id": "c1008cf3",
    "metadata": {},
    "source": [
     "The output of this `print()` statement is telling us that this (simulated) dataset has 64 diffusion-weighted samples.\n",
@@ -169,7 +169,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d847c2cd",
+   "id": "e2f7d9c4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -183,7 +183,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ddc3a0c0",
+   "id": "e4089417",
    "metadata": {},
    "source": [
     "In this case, the dataset is reporting to have 102 diffusion-weighted samples.\n",
@@ -195,7 +195,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1f196426",
+   "id": "93fde81e",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -204,7 +204,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7d4916b9",
+   "id": "c9d41046",
    "metadata": {},
    "source": [
     "Perhaps, the most interesting aspect of our DWI data structure is that it allows indexed access.\n",
@@ -214,7 +214,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "015c51be",
+   "id": "3cc07497",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -225,7 +225,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8562ddb6",
+   "id": "ccb3d63c",
    "metadata": {},
    "source": [
     "## Visualizing the data\n",
@@ -246,7 +246,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "58ab5fd5",
+   "id": "066f1f84",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -261,7 +261,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0ba86437",
+   "id": "9b961d6c",
    "metadata": {},
    "source": [
     "When calling `plot_dwi()`, we will be required a 3D data object, and optionally, an `affine` orientation matrix and a `gradient` or b-vector.\n",
@@ -281,7 +281,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1b673a7a",
+   "id": "30984326",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -296,7 +296,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "38211d1a",
+   "id": "453f2679",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -310,7 +310,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "03d34457",
+   "id": "7c428553",
    "metadata": {},
    "source": [
     "Diffusion that exhibits directionality in the same direction as the gradient results in a loss of signal.\n",
@@ -334,7 +334,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6987b941",
+   "id": "972705d7",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -347,7 +347,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "7d69cd66",
+   "id": "5b9e0e9b",
    "metadata": {},
    "source": [
     "We get a $4\\times102$ -- three spatial coordinates ($b_x$, $b_y$, $b_z$) of the unit-norm \"*b-vector*\", plus the gradient sensitization magnitude (the \"*b-value*\"), with a total of 102 different orientations for the case at hand.\n",
@@ -363,7 +363,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b93fd080",
+   "id": "59a83019",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -376,7 +376,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fb177e95",
+   "id": "f70113b9",
    "metadata": {},
    "source": [
     "Later, we'll refer to this array as the gradient table.\n",
@@ -395,7 +395,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d2d62ef9",
+   "id": "e1c9d481",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -406,7 +406,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6c418921",
+   "id": "ae9e36ee",
    "metadata": {},
    "source": [
     "We've projected all of the gradient directions onto the surface of a sphere, with each unique gradient strength colour-coded.\n",