Summary and Setup

This is a new lesson built with The Carpentries Workbench.

Github setup

  1. You might have already a GitHub, otherwise please create one
  2. Generate your SSH keys as suggested here
  3. Clone the repository by typing (or copying) the following lines in a terminal
git clone git@github.com:HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course.git

Dataset

Download the data zip file and unzip it to your Desktop

CT-vs-PET-Ventilation-Imaging

CT Ventilation as a Functional Imaging Modality for Lung Cancer Radiotherapy from TCIA. We recommend to focus on exhale/inhale breath hold CT (BHCT) Dicoms. Bare in mind that: * The BHCT scans for CT-PET-VI-02 & CT-PET-VI-03 show very little motion between inhale and exhale * The BHCT scans for CT-PET-VI-05 have a different number of slices between the inhale and exhale

Extracting and renaming data paths

Original data directory paths for this work were renamed for easy interpretability as follows:
* 5.000000-Thorax Insp 2.0 B* renamed as inhale_BH_CT
* 7.000000-Thorax Exp 2.0 B* renamed as exhale_BH_CT
* 3.000000-CT Lung 3.0 B* renamed as CT_for_PET
* 4.000000-Galligas Lung-0* renamed as PET

See how the original data paths and renamed paths look like

BASH 

#Original directory paths
/CT-PET-VI-02$ tree -d 
.
├── 1000.000000-PET SUV Factors-26496 [1 item, with size 42.1 kB]
├── 3.000000-CT Lung  3.0  B31f-61322  [175 items, totalling 92.4 MB]
├── 4.000000-Galligas Lung-03537 [159 items, totalling 51.5 MB]
├── 5.000000-Thorax Insp  2.0  B70f-29873 [167 items, totalling 88.1 MB]
├── 7.000000-Thorax Exp  2.0  B70f-73355 [167 items, totalling 88.1 MB]
└── 8.000000-RespLow  2.0  B30s  80  Ex - 100  In-44317 [810 items, totalling 426.9 MB]
#Renamed directory paths
.
├── CT-PET-VI-02
│   ├── CT_for_PET
│   ├── exhale_BH_CT
│   ├── inhale_BH_CT
│   └── PET




#Original directory paths
/CT-PET-VI-03$ tree -d
.
├── 06-25-1996-RTRTRespLowBreathRateRNS Adult-43080
│   ├── 1000.000000-PET SUV Factors-06580
│   ├── 3.000000-CT Lung  3.0  B31f-08354
│   └── 4.000000-Galligas Lung-15379
└── 06-25-1996-RTRTRespLowBreathRateRNS Adult-87093
    ├── 5.000000-Thorax Insp  2.0  B70f-42000
    ├── 7.000000-Thorax Exp  2.0  B70f-45310
    └── 8.000000-RespLow  2.0  B30s  80  Ex - 100  In-54790
#Renamed directory paths for `06-25-1996-RTRTRespLowBreathRateRNS Adult-43080`
├── CT-PET-VI-03
│   ├── CT_for_PET
│   └── PET





#Original directory paths
/CT-PET-VI-05$ tree -d
└── 12-10-1996-RTRTRespLowBreathRateRNS Adult-37585
    ├── 1000.000000-PET SUV Factors-63910
    ├── 3.000000-CT Lung  3.0  B31f-90638
    ├── 4.000000-Galligas Lung-26361
    ├── 5.000000-Thorax Insp  2.0  B70f-45546
    ├── 7.000000-Thorax Exp  2.0  B70f-31579
    └── 8.000000-RespLow  2.0  B30s  80  Ex - 100  In-16454
#Renamed directory paths
├── CT-PET-VI-05
│   ├── CT_for_PET
│   ├── exhale_BH_CT
│   ├── inhale_BH_CT
│   └── PET





#Original directory paths
/CT-PET-VI-07$ tree -d
.
└── 02-14-1997-RTRTRespLowBreathRateRNS Adult-80512
    ├── 1000.000000-PET SUV Factors-99730
    ├── 4.000000-Galligas Lung-82849
    ├── 5.000000-Thorax Insp  2.0  B70f-20440
    ├── 7.000000-Thorax Exp  2.0  B70f-03567
    └── 8.000000-RespLow  2.0  B30s  80  Ex - 100  In-01782
#Renamed directory paths
└── CT-PET-VI-07
    ├── exhale_BH_CT
    ├── inhale_BH_CT
    └── PET

Software Setup

Installing Dependencies in Python Virtual environments

Installing python virtual environment with dependencies (e.g., nibabel, etc). See further instructions here.

Using conda

BASH 

conda create -n "mirVE" python=3.11 pip -c conda-forge
conda config --set pip_interop_enabled True
conda activate mirVE
cd ~/_dependencies
pip install -r requirements.txt

Using python virtual environment

BASH 

# Installing dependencies in Ubuntu 22.04
sudo apt-get install -y python3-pip
sudo apt-get install -y python3-venv
# Create path for venv
cd $HOME
mkdir mirVE
cd mirVE
# Create virtual environment
python3 -m venv mirVE
source mirVE/bin/activate
cd ~/_dependencies
python3 -m pip install -r requirements.txt

ITK-Snap

Hardware Requirements

  • Memory: “Overall 2Gb of memory should be enough for most users; 4Gb should suffice for users with large images.” 🔗
  • Multi - Operating System:
    • ITK-SNAP binaries are distributed for Linux (32 and 64 bit)),
    • Windows (64 bit),
    • and MacOS Leopard (64 bit).

Installation

Installing ITK-SNAP in differen operating systems

  • Open your Terminal to install it

BASH 

sudo apt-get install tree # to visualise files and paths
FILENAME=itksnap-nightly-rel_4.0-Linux-gcc64.tar.gz  #Length: 200943059 (192M) [application/x-gzip]
cd ~/Downloads/
mkdir -p itksnap && cd itksnap
wget https://sourceforge.net/projects/itk-snap/files/itk-snap/Nightly/$FILENAME/download -O $FILENAME
tar -xvzf $FILENAME
  • Open the following link: https://sourceforge.net/projects/itk-snap/files/itk-snap/4.2.0/ and download itksnap-4.2.0-20240422-Darwin-x86_64.dmg
  • Double click the icon for the file you downloaded (e.g., itksnap-3.2.0-rc2-20140919-MacOS-x86_64.dmg).
  • Drag the icon ITK-SNAP.app to the Applications folder.
  • Drag the icon itksnap on top of the icon usr_local_bin in that folder.
  • To add the ITK-SNAP launcher to your Dock, open the Applications folder and drag the ITK-SNAP.app icon onto the dock.