deploy: 5f2f7f1

Author: oesteban

_sources/extra/nifti.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "912a2917",
+   "id": "6d977a72",
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    "source": [
     "# The extra mile\n",
@@ -16,7 +16,7 @@
   {
    "cell_type": "code",
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-   "id": "ae502153",
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    "source": [
@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "dcc0f13a",
+   "id": "e1d722b9",
    "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": "acbad534",
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@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d9ed6265",
+   "id": "de1517f9",
    "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,
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    "outputs": [
     {
@@ -121,7 +121,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3a089477",
+   "id": "3275d64b",
    "metadata": {},
    "source": [
     "### 2. Data\n",
@@ -134,7 +134,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "f3a21503",
+   "id": "174ffe9a",
    "metadata": {
     "tags": [
      "output_scroll"
@@ -465,7 +465,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ce4ea980",
+   "id": "b0b91bf1",
    "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": "93824726",
+   "id": "f5a69d55",
    "metadata": {},
    "outputs": [
     {
@@ -494,7 +494,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "08742922",
+   "id": "64fd0f27",
    "metadata": {},
    "source": [
     "The data is a multidimensional **array** representing the image data.\n",
@@ -505,7 +505,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "2c07aef2",
+   "id": "1ae2ae27",
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    "outputs": [
     {
@@ -525,7 +525,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e3a2c400",
+   "id": "717ec012",
    "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": "bf9bc619",
+   "id": "bda02931",
    "metadata": {},
    "outputs": [
     {
@@ -556,7 +556,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "34eeca8b",
+   "id": "9b8d07fd",
    "metadata": {},
    "source": [
     "This tells us that the image is 128, 128, 66\n",
@@ -567,7 +567,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "f5c5bec1",
+   "id": "b764eba6",
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     "tags": [
      "output_scroll"
@@ -689,7 +689,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "1e63a707",
+   "id": "7a9c29e0",
    "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": "65d2f652",
+   "id": "5e110e41",
    "metadata": {},
    "outputs": [
     {
@@ -725,7 +725,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "75870701",
+   "id": "efc733ef",
    "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": "c319295b",
+   "id": "4a993631",
    "metadata": {},
    "source": [
     "# The problem of head-motion in dMRI"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "28181ed4",
+   "id": "c3fa6542",
    "metadata": {
     "tags": [
      "remove-cell"
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "db1a9790",
+   "id": "eab5f319",
    "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": "3a5b45cb",
+   "id": "43287a59",
    "metadata": {
     "tags": [
      "remove-input"
@@ -54,7 +54,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "328cc736",
+   "id": "cb3a49cf",
    "metadata": {},
    "source": [
     "## Dimensions of the head-motion problem\n",