DOC: Document the PET notebook

Document the PET notebook: add markdown cells explaining the steps.

Author: jhlegarreta

docs/notebooks/pet_motion_estimation.ipynb

@@ -1,11 +1,31 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "4111cc1b-5123-407a-8ec6-56d65bc94bc4",
    "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "# Positron emission tomography (PET) data realignment example\n",
+    "\n",
+    "This example shows how to estimate the head motion of a PET dataset using\n",
+    "`NiFreeze`.\n",
+    "\n",
+    "The notebook uses the `sub-02` dataset that was generated synthetically from\n",
+    "a real PET dataset by adding random motion. The dataset can be installed\n",
+    "from [GIN G-node](https://gin.g-node.org/nipreps-data/tests-nifreeze):\n",
+    "\n",
+    "```\n",
+    "$ datalad install -g https://gin.g-node.org/nipreps-data/tests-nifreeze.git\n",
+    "```\n",
+    "\n",
+    "after which the environment variable `TEST_DATA_HOME` will need to be set to point to the corresponding folder.\n"
+   ],
+   "id": "e0f292c6b783bafa"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
    "outputs": [],
+   "execution_count": 1,
    "source": [
     "from os import getenv\n",
     "from pathlib import Path\n",
@@ -30,7 +50,8 @@
     ")\n",
     "\n",
     "pet_dataset = PET.load(pet_file, json_file)"
-   ]
+   ],
+   "id": "6d67b411d3c9330d"
   },
   {
    "cell_type": "code",
@@ -53,6 +74,17 @@
     "pet_dataset"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "## Model fitting and motion correction\n",
+    "\n",
+    "The relevant structure to model PET data is `nifreeze.model.PETModel`. We\n",
+    "instantiate it by providing it with the loaded PET dataset."
+   ],
+   "id": "886c5ca9bd9eb3e4"
+  },
   {
    "cell_type": "code",
    "execution_count": 4,
@@ -421,6 +453,18 @@
     "model.fit_predict(None)"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "Let's now ask the model for a prediction at the `midframe[2]` time point. By\n",
+    "calling `model.fit_predict` the model is fitted using all the available data,\n",
+    "and a prediction is requested on the time provided as the argument. The\n",
+    "B-Spline PET model employs uses a B-Spline-based interpolation method to\n",
+    "estimate the data for the requested frame."
+   ],
+   "id": "cbd738998dd6ed1f"
+  },
   {
    "cell_type": "code",
    "execution_count": 7,
@@ -432,6 +476,15 @@
     "predicted = model.fit_predict(pet_dataset.midframe[index])"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "We now save the uncorrected and corrected data so that we can visualize the\n",
+    "difference."
+   ],
+   "id": "17f3d61720ac0959"
+  },
   {
    "cell_type": "code",
    "execution_count": 8,
@@ -452,6 +505,15 @@
     "nifti_img_after.to_filename(output_path_after)"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "Let's now visualize a number of axial, sagittal and coronal slices of the\n",
+    "uncorrected and corrected data."
+   ],
+   "id": "7126dd0b08f3d70e"
+  },
   {
    "cell_type": "code",
    "execution_count": 10,
@@ -2242,10 +2304,21 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 13,
-   "id": "78edfed2-8200-48be-9f58-8fb910fac299",
    "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "## Motion estimation\n",
+    "\n",
+    "We now want to have an estimate of the motion that the model corrects. We will\n",
+    "need to instantiate the `nifreeze.estimator.PETMotionEstimator`, which will\n",
+    "take an instance of the model. We will call `run` to get the parameters of the\n",
+    "affine transform estimation."
+   ],
+   "id": "44d029b581d72b55"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
    "outputs": [
     {
      "name": "stderr",
@@ -2255,6 +2328,7 @@
      ]
     }
    ],
+   "execution_count": 13,
    "source": [
     "from nifreeze.estimator import PETMotionEstimator\n",
     "\n",
@@ -2265,7 +2339,8 @@
     "    pet_dataset,\n",
     "    omp_nthreads=4,\n",
     ")"
-   ]
+   ],
+   "id": "af6ca1ccbce1e579"
   },
   {
    "cell_type": "code",
@@ -2427,6 +2502,15 @@
     "affines"
    ]
   },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": [
+    "Let's now visualize the estimated motion: we will plot the translation and\n",
+    "rotation components in the affine transform for each axis."
+   ],
+   "id": "79a4b84912aed9f9"
+  },
   {
    "metadata": {},
    "cell_type": "code",
@@ -2537,14 +2621,6 @@
     "\n",
     "plt.show()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "14308ff4-d5b1-4270-aca2-0d7e9ccef27f",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {