Update tutorial notebooks

Author: github-actions[bot]

docs/notebook/01-intro.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "daf53a4b",
+   "id": "c319295b",
    "metadata": {},
    "source": [
     "# The problem of head-motion in dMRI"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15b354de",
+   "id": "28181ed4",
    "metadata": {
     "tags": [
      "remove-cell"
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d34d8f90",
+   "id": "db1a9790",
    "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": "a41bdab4",
+   "id": "3a5b45cb",
    "metadata": {
     "tags": [
      "remove-input"
@@ -54,7 +54,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9d7f68b7",
+   "id": "328cc736",
    "metadata": {},
    "source": [
     "## Dimensions of the head-motion problem\n",

docs/notebook/02-data.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "df575a24",
+   "id": "27909aa8",
    "metadata": {},
    "source": [
     "# Introduction to dMRI data"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8b8fb9a7",
+   "id": "4fe93af9",
    "metadata": {
     "tags": [
      "remove-cell"
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0e8a9d9c",
+   "id": "9b4f1411",
    "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": "160507ad",
+   "id": "50d8f982",
    "metadata": {
     "tags": [
      "remove-input"
@@ -53,7 +53,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "79022185",
+   "id": "de9273c6",
    "metadata": {},
    "source": [
     "*Sourced from Dr. A. Rokem, DIPY Workshop 2021*\n",
@@ -86,7 +86,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e54d4d34",
+   "id": "6c11a93a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -124,7 +124,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fda0e7ac",
+   "id": "522af7c1",
    "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": "185586b7",
+   "id": "ad8c9add",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -152,7 +152,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b6907093",
+   "id": "130ddd11",
    "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": "ac308f08",
+   "id": "ce753a17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -183,7 +183,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2d4eb7d4",
+   "id": "af366c94",
    "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": "9fd17434",
+   "id": "5ca082ee",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -204,7 +204,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "cb1c399a",
+   "id": "b6b803f6",
    "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": "87a38a30",
+   "id": "dc56d075",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -225,7 +225,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8923985c",
+   "id": "2f975182",
    "metadata": {},
    "source": [
     "## Visualizing the data\n",
@@ -246,7 +246,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "289cecc4",
+   "id": "e9756cfc",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -261,7 +261,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "16658d1c",
+   "id": "38729846",
    "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": "95997e60",
+   "id": "ce346932",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -296,7 +296,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6d566c4d",
+   "id": "07ce2186",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -310,7 +310,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "5b8134f2",
+   "id": "d34906ad",
    "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": "31dc8bd3",
+   "id": "833a8fc8",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -347,7 +347,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "383e4803",
+   "id": "4cef8f79",
    "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": "00d4c0d4",
+   "id": "7cd4b77a",
    "metadata": {
     "tags": [
      "hide-cell"
@@ -376,7 +376,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6ef78f79",
+   "id": "1f4f4a35",
    "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": "9c093513",
+   "id": "d43ed401",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -406,7 +406,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "cb580c80",
+   "id": "bd8d8aa7",
    "metadata": {},
    "source": [
     "We've projected all of the gradient directions onto the surface of a sphere, with each unique gradient strength colour-coded.\n",