HealthBioscienceIDEAS · jamie-mcclelland · Jan 13, 2025 · Jan 16, 2025 · Feb 3, 2025 · Feb 3, 2025
diff --git a/config.yaml b/config.yaml
@@ -12,7 +12,7 @@
 carpentry: 'IDEAS'
 
 # Overall title for pages.
-title: 'Medical-Image-Registration-Short-Course'
+title: 'MPHY0025 IPMI Registration Practical Exercises Instructions'
 
 # Date the lesson was created (YYYY-MM-DD, this is empty by default)
 created: '2024-05-13'

diff --git a/episodes/fig/CT-PET-VI-02.svg b/episodes/fig/CT-PET-VI-02.svg
diff --git a/episodes/fig/Figure_1.png b/episodes/fig/Figure_1.png
diff --git a/episodes/fig/colour-map-editor.png b/episodes/fig/colour-map-editor.png
diff --git a/episodes/fig/final_output.png b/episodes/fig/final_output.png
diff --git a/episodes/fig/final_results_vid.mp4 b/episodes/fig/final_results_vid.mp4
diff --git a/episodes/fig/image-info.png b/episodes/fig/image-info.png
diff --git a/episodes/fig/itk-snap-16-32-bits.svg b/episodes/fig/itk-snap-16-32-bits.svg
diff --git a/episodes/fig/itk-snap-additional-image.png b/episodes/fig/itk-snap-additional-image.png
diff --git a/episodes/fig/itk-snap-calculating-registrations.png b/episodes/fig/itk-snap-calculating-registrations.png
diff --git a/episodes/fig/itk-snap-colour-overlay-as-semi-transparent-image.svg b/episodes/fig/itk-snap-colour-overlay-as-semi-transparent-image.svg
diff --git a/episodes/fig/itk-snap-colour-overlay-as-separate-image.svg b/episodes/fig/itk-snap-colour-overlay-as-separate-image.svg
diff --git a/episodes/fig/itk-snap-image-manual-registration.png b/episodes/fig/itk-snap-image-manual-registration.png
diff --git a/episodes/fig/itk-snap-layer-inspector-color-map-tab.png b/episodes/fig/itk-snap-layer-inspector-color-map-tab.png
diff --git a/episodes/fig/itk-snap-layer-inspector-contrast-tab.png b/episodes/fig/itk-snap-layer-inspector-contrast-tab.png
diff --git a/episodes/fig/itk-snap-layer-inspector-general-tab.png b/episodes/fig/itk-snap-layer-inspector-general-tab.png
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diff --git a/episodes/fig/itk-snap-layer-inspector-metadata-tab.png b/episodes/fig/itk-snap-layer-inspector-metadata-tab.png
diff --git a/episodes/fig/itk-snap-main-window.svg b/episodes/fig/itk-snap-main-window.svg
diff --git a/episodes/fig/itk-snap-opening-dicoms.svg b/episodes/fig/itk-snap-opening-dicoms.svg
diff --git a/episodes/fig/itk-snap-overlay-semi-transparent-cropped-affine.png b/episodes/fig/itk-snap-overlay-semi-transparent-cropped-affine.png
diff --git a/episodes/fig/itk-snap-save-ct-for-pet.png b/episodes/fig/itk-snap-save-ct-for-pet.png
diff --git a/episodes/fig/itk-snap-thumbnails.png b/episodes/fig/itk-snap-thumbnails.png
diff --git a/episodes/fig/itk-snap-tools-reorient-image.png b/episodes/fig/itk-snap-tools-reorient-image.png
diff --git a/episodes/fig/itk-snap-viewing-dicoms.svg b/episodes/fig/itk-snap-viewing-dicoms.svg
diff --git a/episodes/fig/itk-snap_ct_for_pet_cropped_nii_gz.png b/episodes/fig/itk-snap_ct_for_pet_cropped_nii_gz.png
diff --git a/episodes/fig/layers-panel.png b/episodes/fig/layers-panel.png
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diff --git a/episodes/fig/new-itk-snap-window.png b/episodes/fig/new-itk-snap-window.png
diff --git a/episodes/fig/open-additional-image.png b/episodes/fig/open-additional-image.png
diff --git a/episodes/fig/overlay-wizard.png b/episodes/fig/overlay-wizard.png
diff --git a/episodes/fig/p4-comp-jac.png b/episodes/fig/p4-comp-jac.png
diff --git a/episodes/fig/p4-def-field-comp.png b/episodes/fig/p4-def-field-comp.png
diff --git a/episodes/fig/p4-def-field-zoom.png b/episodes/fig/p4-def-field-zoom.png
diff --git a/episodes/fig/p4-reg-output-numlev1.png b/episodes/fig/p4-reg-output-numlev1.png
diff --git a/episodes/fig/p4-reg-output-sigelastic0.5.png b/episodes/fig/p4-reg-output-sigelastic0.5.png
diff --git a/episodes/fig/p4-reg-output-sigelastic0.png b/episodes/fig/p4-reg-output-sigelastic0.png
diff --git a/episodes/fig/p4-reg-output-sigfluid0.png b/episodes/fig/p4-reg-output-sigfluid0.png
diff --git a/episodes/fig/p4-reg-output.png b/episodes/fig/p4-reg-output.png
diff --git a/episodes/fig/p4-reg-output2-numlev1.png b/episodes/fig/p4-reg-output2-numlev1.png
diff --git a/episodes/fig/p4-reg-output2-sigelastic0.5.png b/episodes/fig/p4-reg-output2-sigelastic0.5.png
diff --git a/episodes/fig/p4-reg-output2-sigelastic0.png b/episodes/fig/p4-reg-output2-sigelastic0.png
diff --git a/episodes/fig/p4-reg-output2-sigfluid0.png b/episodes/fig/p4-reg-output2-sigfluid0.png
diff --git a/episodes/fig/p4-reg-output2.png b/episodes/fig/p4-reg-output2.png
diff --git a/episodes/fig/itk-snap-additional-image-1.png → ...des/fig/practical1-additional-image-1.png b/episodes/fig/itk-snap-additional-image-1.png → ...des/fig/practical1-additional-image-1.png
diff --git a/episodes/fig/itk-snap-additional-image-2.png → ...des/fig/practical1-additional-image-2.png b/episodes/fig/itk-snap-additional-image-2.png → ...des/fig/practical1-additional-image-2.png
diff --git a/episodes/fig/itk-snap-additional-image-3.png → ...des/fig/practical1-additional-image-3.png b/episodes/fig/itk-snap-additional-image-3.png → ...des/fig/practical1-additional-image-3.png
diff --git a/episodes/fig/itk-snap-additional-image-4.png → ...des/fig/practical1-additional-image-4.png b/episodes/fig/itk-snap-additional-image-4.png → ...des/fig/practical1-additional-image-4.png
diff --git a/episodes/fig/itk-snap-additional-image-5.png → ...des/fig/practical1-additional-image-5.png b/episodes/fig/itk-snap-additional-image-5.png → ...des/fig/practical1-additional-image-5.png
diff --git a/episodes/fig/itk-snap-additional-image-6.png → ...des/fig/practical1-additional-image-6.png b/episodes/fig/itk-snap-additional-image-6.png → ...des/fig/practical1-additional-image-6.png
diff --git a/episodes/fig/itk-snap-aligned-images-1.png → episodes/fig/practical1-aligned-images-1.png b/episodes/fig/itk-snap-aligned-images-1.png → episodes/fig/practical1-aligned-images-1.png
diff --git a/episodes/fig/itk-snap-aligned-images-2.png → episodes/fig/practical1-aligned-images-2.png b/episodes/fig/itk-snap-aligned-images-2.png → episodes/fig/practical1-aligned-images-2.png
diff --git a/...des/fig/itk-snap-cropped-ct-aligned-1.png → ...s/fig/practical1-cropped-ct-aligned-1.png b/...des/fig/itk-snap-cropped-ct-aligned-1.png → ...s/fig/practical1-cropped-ct-aligned-1.png
diff --git a/...des/fig/itk-snap-cropped-ct-aligned-2.png → ...s/fig/practical1-cropped-ct-aligned-2.png b/...des/fig/itk-snap-cropped-ct-aligned-2.png → ...s/fig/practical1-cropped-ct-aligned-2.png
diff --git a/episodes/fig/itk-snap-cropped-ct.png → episodes/fig/practical1-cropped-ct.png b/episodes/fig/itk-snap-cropped-ct.png → episodes/fig/practical1-cropped-ct.png
diff --git a/episodes/fig/itk-snap-ct-pet-overlay.png → episodes/fig/practical1-ct-pet-overlay.png b/episodes/fig/itk-snap-ct-pet-overlay.png → episodes/fig/practical1-ct-pet-overlay.png
diff --git a/episodes/fig/itk-snap-cursor-inspector.png → episodes/fig/practical1-cursor-inspector.png b/episodes/fig/itk-snap-cursor-inspector.png → episodes/fig/practical1-cursor-inspector.png
diff --git a/...-snap-image-layer-inspector-color-map.png → ...ical1-image-layer-inspector-color-map.png b/...-snap-image-layer-inspector-color-map.png → ...ical1-image-layer-inspector-color-map.png
diff --git a/...k-snap-image-layer-inspector-contrast.png → ...tical1-image-layer-inspector-contrast.png b/...k-snap-image-layer-inspector-contrast.png → ...tical1-image-layer-inspector-contrast.png
diff --git a/...tk-snap-image-layer-inspector-general.png → ...ctical1-image-layer-inspector-general.png b/...tk-snap-image-layer-inspector-general.png → ...ctical1-image-layer-inspector-general.png
diff --git a/...g/itk-snap-image-layer-inspector-info.png → ...practical1-image-layer-inspector-info.png b/...g/itk-snap-image-layer-inspector-info.png → ...practical1-image-layer-inspector-info.png
diff --git a/...k-snap-image-layer-inspector-metadata.png → ...tical1-image-layer-inspector-metadata.png b/...k-snap-image-layer-inspector-metadata.png → ...tical1-image-layer-inspector-metadata.png
diff --git a/episodes/fig/itk-snap-info-16.png → episodes/fig/practical1-info-16.png b/episodes/fig/itk-snap-info-16.png → episodes/fig/practical1-info-16.png
diff --git a/episodes/fig/itk-snap-info-32.png → episodes/fig/practical1-info-32.png b/episodes/fig/itk-snap-info-32.png → episodes/fig/practical1-info-32.png
diff --git a/.../fig/itk-snap-inhale-and-exhale-scans.png → ...ig/practical1-inhale-and-exhale-scans.png b/.../fig/itk-snap-inhale-and-exhale-scans.png → ...ig/practical1-inhale-and-exhale-scans.png
diff --git a/episodes/fig/itk-snap-inhale-scan.png → episodes/fig/practical1-inhale-scan.png b/episodes/fig/itk-snap-inhale-scan.png → episodes/fig/practical1-inhale-scan.png
diff --git a/...des/fig/itk-snap-layout-pref-reminder.png → ...s/fig/practical1-layout-pref-reminder.png b/...des/fig/itk-snap-layout-pref-reminder.png → ...s/fig/practical1-layout-pref-reminder.png
diff --git a/episodes/fig/itk-snap-metadata-16.png → episodes/fig/practical1-metadata-16.png b/episodes/fig/itk-snap-metadata-16.png → episodes/fig/practical1-metadata-16.png
diff --git a/episodes/fig/itk-snap-metadata-32.png → episodes/fig/practical1-metadata-32.png b/episodes/fig/itk-snap-metadata-32.png → episodes/fig/practical1-metadata-32.png
diff --git a/episodes/fig/itk-snap-misaligned-images.png → ...odes/fig/practical1-misaligned-images.png b/episodes/fig/itk-snap-misaligned-images.png → ...odes/fig/practical1-misaligned-images.png
diff --git a/episodes/fig/itk-snap-nifti-header.png → episodes/fig/practical1-nifti-header.png b/episodes/fig/itk-snap-nifti-header.png → episodes/fig/practical1-nifti-header.png
diff --git a/episodes/fig/itk-snap-open-image-1.png → episodes/fig/practical1-open-image-1.png b/episodes/fig/itk-snap-open-image-1.png → episodes/fig/practical1-open-image-1.png
diff --git a/episodes/fig/itk-snap-open-image-2.png → episodes/fig/practical1-open-image-2.png b/episodes/fig/itk-snap-open-image-2.png → episodes/fig/practical1-open-image-2.png
diff --git a/episodes/fig/itk-snap-open-image-3.png → episodes/fig/practical1-open-image-3.png b/episodes/fig/itk-snap-open-image-3.png → episodes/fig/practical1-open-image-3.png
diff --git a/episodes/fig/itk-snap-recent-images.png → episodes/fig/practical1-recent-images.png b/episodes/fig/itk-snap-recent-images.png → episodes/fig/practical1-recent-images.png
diff --git a/episodes/fig/itk-snap-save-image-1.png → episodes/fig/practical1-save-image-1.png b/episodes/fig/itk-snap-save-image-1.png → episodes/fig/practical1-save-image-1.png
diff --git a/...des/fig/trans_rot_final_image_pad0_nn.gif → episodes/fig/practical2-NN-anim.gif b/...des/fig/trans_rot_final_image_pad0_nn.gif → episodes/fig/practical2-NN-anim.gif
diff --git a/episodes/fig/trans_rot_image_nn_spline.png → episodes/fig/practical2-NN-spline-final.png b/episodes/fig/trans_rot_image_nn_spline.png → episodes/fig/practical2-NN-spline-final.png
diff --git a/...trans_rot_final_image_compose_nearest.gif → episodes/fig/practical2-comp-NN-anim.gif b/...trans_rot_final_image_compose_nearest.gif → episodes/fig/practical2-comp-NN-anim.gif
diff --git a/.../trans_rot_final_image_compose_linear.gif → episodes/fig/practical2-comp-linear-anim.gif b/.../trans_rot_final_image_compose_linear.gif → episodes/fig/practical2-comp-linear-anim.gif
diff --git a/...ans_rot_final_image_compose_splinef2d.gif → episodes/fig/practical2-comp-spline-anim.gif b/...ans_rot_final_image_compose_splinef2d.gif → episodes/fig/practical2-comp-spline-anim.gif
diff --git a/episodes/fig/trans_diff_image_intlims.png → ...g/practical2-diff-image-half-int-lims.png b/episodes/fig/trans_diff_image_intlims.png → ...g/practical2-diff-image-half-int-lims.png
diff --git a/episodes/fig/trans_diff_image_10.5.png → episodes/fig/practical2-diff-image-half.png b/episodes/fig/trans_diff_image_10.5.png → episodes/fig/practical2-diff-image-half.png
diff --git a/episodes/fig/trans_diff_image.png → episodes/fig/practical2-diff-image-whole.png b/episodes/fig/trans_diff_image.png → episodes/fig/practical2-diff-image-whole.png
diff --git a/episodes/fig/trans_rot_final_image_pad0.gif → episodes/fig/practical2-pad0-anim.gif b/episodes/fig/trans_rot_final_image_pad0.gif → episodes/fig/practical2-pad0-anim.gif
diff --git a/episodes/fig/trans_rot_final_image_pad0.png → episodes/fig/practical2-pad0-final.png b/episodes/fig/trans_rot_final_image_pad0.png → episodes/fig/practical2-pad0-final.png
diff --git a/episodes/fig/trans_rot_final_image.gif → episodes/fig/practical2-padnan-anim.gif b/episodes/fig/trans_rot_final_image.gif → episodes/fig/practical2-padnan-anim.gif
diff --git a/episodes/fig/trans_rot_final_image.png → episodes/fig/practical2-padnan-final.png b/episodes/fig/trans_rot_final_image.png → episodes/fig/practical2-padnan-final.png
diff --git a/episodes/fig/trans_rot_final_image_push.gif → episodes/fig/practical2-push-anim.gif b/episodes/fig/trans_rot_final_image_push.gif → episodes/fig/practical2-push-anim.gif
diff --git a/episodes/fig/trans_disp_image.png → ...des/fig/practical2-reorientated-image.png b/episodes/fig/trans_disp_image.png → ...des/fig/practical2-reorientated-image.png
diff --git a/episodes/fig/trans_rot_image.png → episodes/fig/practical2-rotated-image.png b/episodes/fig/trans_rot_image.png → episodes/fig/practical2-rotated-image.png
diff --git a/...fig/trans_rot_final_image_pad0_spline.gif → episodes/fig/practical2-spline-anim.gif b/...fig/trans_rot_final_image_pad0_spline.gif → episodes/fig/practical2-spline-anim.gif
diff --git a/episodes/fig/trans_disp_image_translated.png → episodes/fig/practical2-translated-image.png b/episodes/fig/trans_disp_image_translated.png → episodes/fig/practical2-translated-image.png
diff --git a/episodes/fig/p3-entropies-values.png → episodes/fig/practical3-entropies-values.png b/episodes/fig/p3-entropies-values.png → episodes/fig/practical3-entropies-values.png
diff --git a/episodes/fig/p3-images.png → episodes/fig/practical3-images.png b/episodes/fig/p3-images.png → episodes/fig/practical3-images.png
diff --git a/episodes/fig/practical3-in-out-alignment-anim.gif b/episodes/fig/practical3-in-out-alignment-anim.gif
diff --git a/episodes/fig/p3-int8-intensities.png → episodes/fig/practical3-int8-intensities.png b/episodes/fig/p3-int8-intensities.png → episodes/fig/practical3-int8-intensities.png
diff --git a/episodes/fig/p3-mi-values.png → episodes/fig/practical3-mi-values.png b/episodes/fig/p3-mi-values.png → episodes/fig/practical3-mi-values.png
diff --git a/episodes/fig/p3-msd-values.png → episodes/fig/practical3-msd-values.png b/episodes/fig/p3-msd-values.png → episodes/fig/practical3-msd-values.png
diff --git a/episodes/fig/p3-ncc-values.png → episodes/fig/practical3-ncc-values.png b/episodes/fig/p3-ncc-values.png → episodes/fig/practical3-ncc-values.png
diff --git a/episodes/fig/p3-nmi-values.png → episodes/fig/practical3-nmi-values.png b/episodes/fig/p3-nmi-values.png → episodes/fig/practical3-nmi-values.png
diff --git a/episodes/fig/p3-rotated-image.png → episodes/fig/practical3-rotated-image.png b/episodes/fig/p3-rotated-image.png → episodes/fig/practical3-rotated-image.png
diff --git a/episodes/fig/p3-ssd-values.png → episodes/fig/practical3-ssd-values.png b/episodes/fig/p3-ssd-values.png → episodes/fig/practical3-ssd-values.png
diff --git a/episodes/fig/practical4-comp-def-field-jac.png b/episodes/fig/practical4-comp-def-field-jac.png
diff --git a/episodes/fig/practical4-comp-final.png b/episodes/fig/practical4-comp-final.png
diff --git a/episodes/fig/practical4-def-field-zoom.png b/episodes/fig/practical4-def-field-zoom.png
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diff --git a/episodes/fig/practical4-defparams-final.png b/episodes/fig/practical4-defparams-final.png
diff --git a/episodes/fig/p4-reg-first-step.png → episodes/fig/practical4-defparams-start.png b/episodes/fig/p4-reg-first-step.png → episodes/fig/practical4-defparams-start.png
diff --git a/episodes/fig/p4-diff-images.png → episodes/fig/practical4-diff-images.png b/episodes/fig/p4-diff-images.png → episodes/fig/practical4-diff-images.png
diff --git a/episodes/fig/practical4-elastic0-final.png b/episodes/fig/practical4-elastic0-final.png
diff --git a/episodes/fig/practical4-elastic05-final-jac.png b/episodes/fig/practical4-elastic05-final-jac.png
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diff --git a/episodes/fig/practical4-fig-controls.png b/episodes/fig/practical4-fig-controls.png
diff --git a/episodes/fig/practical4-fluid0-end.png b/episodes/fig/practical4-fluid0-end.png
diff --git a/episodes/fig/practical4-fluid0-final.png b/episodes/fig/practical4-fluid0-final.png
diff --git a/episodes/fig/p4-displayed-images.png → episodes/fig/practical4-images.png b/episodes/fig/p4-displayed-images.png → episodes/fig/practical4-images.png
diff --git a/episodes/fig/p4-jac-binarymask.png → episodes/fig/practical4-jac-binarymask.png b/episodes/fig/p4-jac-binarymask.png → episodes/fig/practical4-jac-binarymask.png
diff --git a/episodes/fig/practical4-numlev1-final.png b/episodes/fig/practical4-numlev1-final.png
diff --git a/episodes/fig/registration_animation.gif b/episodes/fig/registration_animation.gif
diff --git a/episodes/fig/registration_animation_comp.gif b/episodes/fig/registration_animation_comp.gif
diff --git a/episodes/fig/registration_animation_elastic0.5fluid1.gif b/episodes/fig/registration_animation_elastic0.5fluid1.gif
diff --git a/episodes/fig/registration_animation_elastic0.gif b/episodes/fig/registration_animation_elastic0.gif
diff --git a/episodes/fig/registration_animation_fluid0.gif b/episodes/fig/registration_animation_fluid0.gif
diff --git a/episodes/fig/registration_animation_level1.gif b/episodes/fig/registration_animation_level1.gif
diff --git a/episodes/fig/rotated_images.gif b/episodes/fig/rotated_images.gif
diff --git a/episodes/fig/itk-snap-install-1.png → episodes/fig/setup-itk-snap-install-1.png b/episodes/fig/itk-snap-install-1.png → episodes/fig/setup-itk-snap-install-1.png
diff --git a/episodes/fig/itk-snap-install-2.png → episodes/fig/setup-itk-snap-install-2.png b/episodes/fig/itk-snap-install-2.png → episodes/fig/setup-itk-snap-install-2.png
diff --git a/episodes/fig/setup-vscode-ipmi-reg-folder.png b/episodes/fig/setup-vscode-ipmi-reg-folder.png
diff --git a/episodes/fig/setup-vscode-select-kernel-install-packages.png b/episodes/fig/setup-vscode-select-kernel-install-packages.png
diff --git a/episodes/fig/setup-vscode-select-kernel-ipmi-reg.png b/episodes/fig/setup-vscode-select-kernel-ipmi-reg.png
diff --git a/episodes/fig/vscode-ideas-reg.png b/episodes/fig/vscode-ideas-reg.png
diff --git a/episodes/fig/vscode-python-env.png b/episodes/fig/vscode-python-env.png
diff --git a/episodes/fig/vscode-select-kernel.png b/episodes/fig/vscode-select-kernel.png
diff --git a/episodes/fig/vscode.png b/episodes/fig/vscode.png
diff --git a/episodes/files/demonsReg.py b/episodes/files/demonsReg.py
diff --git a/episodes/files/ipmi_reg_python_env.yml b/episodes/files/ipmi_reg_python_env.yml
@@ -0,0 +1,11 @@
+name: ideas-reg
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - ipykernel=6.29.5
+  - matplotlib=3.9.2
+  - nibabel=5.3.2
+  - numpy=2.1.3
+  - scikit-image=0.24.0
+  - scipy=1.14.1
diff --git a/episodes/files/practical1_notebook.ipynb b/episodes/files/practical1_notebook.ipynb
@@ -0,0 +1,272 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Practical 1: An introduction to medical imaging data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 1. Visualising images with ITK-SNAP\n",
+    "\n",
+    "#### This section is completed using ITK-SNAP.\n",
+    "\n",
+    "## 2. Viewing and understanding the NIfTI header with NiBabel\n",
+    "\n",
+    "### 2.1. Reading and displaying the NIfTI header"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import packages\n",
+    "import numpy as np\n",
+    "import nibabel as nib"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# load the nifti file saved in section 1\n",
+    "ct_for_pet_nii = nib.load(\"data/practical1/CT_for_PET.nii.gz\")\n",
+    "\n",
+    "#this returns a Nifti1Image object\n",
+    "print(type(ct_for_pet_nii))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# display the size/shape of the image\n",
+    "print(ct_for_pet_nii.shape)\n",
+    "\n",
+    "# display the data type of the image\n",
+    "print(ct_for_pet_nii.get_data_dtype())\n",
+    "\n",
+    "# display the affine matrix for the image\n",
+    "print(ct_for_pet_nii.affine)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# print the header\n",
+    "print(ct_for_pet_nii.header)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 2.2 Specifying the affine transform"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# print the matrix represented by the qform\n",
+    "print(ct_for_pet_nii.get_qform())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 3. Modifying NIfTI images and headers with NiBabel\n",
+    "\n",
+    "### 3.1. Changing the data type and qform code"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# read the image data of the Nifti1Image object\n",
+    "# it gets loaded as a numpy array and casted to float64\n",
+    "ct_for_pet_img = ct_for_pet_nii.get_fdata()\n",
+    "\n",
+    "# check the type of the array\n",
+    "print(type(ct_for_pet_img))\n",
+    "\n",
+    "# check the type of the array elements\n",
+    "print(ct_for_pet_img.dtype)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# change the data type to float32\n",
+    "ct_for_pet_nii.set_data_dtype(np.float32)\n",
+    "\n",
+    "# set the qform code to unkown (0)\n",
+    "ct_for_pet_nii.set_qform(None, code='unknown')\n",
+    "\n",
+    "# check the header has been updated\n",
+    "print(ct_for_pet_nii.header)\n",
+    "\n",
+    "# save the float32 image to disk\n",
+    "nib.save(ct_for_pet_nii, 'data/practical1/CT_for_PET_float32.nii.gz')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Check data types with NiBabel"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# load the new image and check the data type is float32\n",
+    "ct_for_pet_float32_nii = nib.load(\"data/practical1/CT_for_PET_float32.nii.gz\")\n",
+    "print(ct_for_pet_float32_nii.get_data_dtype())\n",
+    "\n",
+    "# load the original image and check the data type is still int16\n",
+    "ct_for_pet_orig_nii = nib.load(\"data/practical1/CT_for_PET.nii.gz\")\n",
+    "print(ct_for_pet_orig_nii.get_data_dtype())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 3.2. Cropping images"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# create a new array containing a copy of the desired slices\n",
+    "x_first = 91\n",
+    "x_last = 390\n",
+    "y_first = 131\n",
+    "y_last = 375\n",
+    "z_first = 21\n",
+    "z_last = 155\n",
+    "ct_for_pet_cropped_img = ct_for_pet_img[x_first:x_last+1, y_first:y_last+1, z_first:z_last+1].copy()\n",
+    "\n",
+    "# check the size of the arrays containing the original image and the cropped image\n",
+    "print(ct_for_pet_img.shape)\n",
+    "print(ct_for_pet_cropped_img.shape)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# create a new Nifti1Image object using the header and affine from the uncropped image\n",
+    "ct_for_pet_cropped_nii = nib.nifti1.Nifti1Image(ct_for_pet_cropped_img, ct_for_pet_nii.affine, ct_for_pet_nii.header)\n",
+    "\n",
+    "# check the shape and header of the new Nifti1Image object\n",
+    "print(ct_for_pet_cropped_nii.shape)\n",
+    "print(ct_for_pet_cropped_nii.header)\n",
+    "\n",
+    "# save the cropped image\n",
+    "nib.save(ct_for_pet_cropped_nii, \"data/practical1/CT_for_PET_cropped.nii.gz\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# calculate the world coordinates of first voxel in the cropped image\n",
+    "cropped_origin = ct_for_pet_nii.affine @ np.array([x_first, y_first, z_first, 1])\n",
+    "print(cropped_origin)\n",
+    "\n",
+    "# use these to update the corresponding values in the affine matrix for the cropped image\n",
+    "ct_for_pet_cropped_nii.affine[0,3] = cropped_origin[0]\n",
+    "ct_for_pet_cropped_nii.affine[1,3] = cropped_origin[1]\n",
+    "ct_for_pet_cropped_nii.affine[2,3] = cropped_origin[2]\n",
+    "print(ct_for_pet_cropped_nii.affine)\n",
+    "\n",
+    "# save the cropped image - this also updates the sform values in the header using the updated affine\n",
+    "print(ct_for_pet_cropped_nii.header.get_sform())\n",
+    "nib.save(ct_for_pet_cropped_nii, \"data/practical1/CT_for_PET_cropped_aligned.nii.gz\")\n",
+    "print(ct_for_pet_cropped_nii.header.get_sform())\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# we can do the same as above using nibabel's slicer attribute\n",
+    "ct_for_pet_slicer_nii = ct_for_pet_nii.slicer[x_first:x_last+1, y_first:y_last+1, z_first:z_last+1]\n",
+    "print(ct_for_pet_slicer_nii.header)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 3.3. Aligning data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 61,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# TODO: Add you code here to align the centre of the inhale_BH_CT with the centre of CT_for_PET\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "ideas-reg",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}