Spinal Cord Toolbox

https://spinalcordtoolbox.com/stable/
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Spinal Cord Toolbox (SCT) is an open-source software package dedicated to the processing and...
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### Model Installation Examples

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/tumor_edema_cavity_t1_t2.html

Examples for installing models using custom URLs and running the segmentation on a T2 image.

```bash
sct_deepseg tumor_edema_cavity_t1_t2 -install -custom-url CUSTOM_URL
```

```bash
sct_deepseg tumor_edema_cavity_t1_t2 -i t2.nii.gz
```

--------------------------------

### Install model with custom URL and run segmentation

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/gm_wm_exvivo_t2.html

Examples showing how to install a specific model version using a custom URL and how to run the segmentation on an input file.

```bash
sct_deepseg gm_wm_exvivo_t2 -install -custom-url CUSTOM_URL
```

```bash
sct_deepseg gm_wm_exvivo_t2 -i t2.nii.gz
```

--------------------------------

### Install custom model and segment image

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/lesion_ms_axial_t2.html

Two example commands: one installs a custom model version using -custom-url, and the other segments an input image with -i.

```bash
sct_deepseg lesion_ms_axial_t2 -install -custom-url CUSTOM_URL
```

```bash
sct_deepseg lesion_ms_axial_t2 -i t2.nii.gz
```

--------------------------------

### Example sct_deepseg spinalcord commands

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/spinalcord.html

Example commands: install a specific model version using -custom-url, and segment an image with -i.

```bash
sct_deepseg spinalcord -install -custom-url CUSTOM_URL
```

```bash
sct_deepseg spinalcord -i t2.nii.gz
```

--------------------------------

### View help and usage examples for sct_deepseg

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/all_tools.html

Shows the help message and lists available tasks. The examples demonstrate how to view help for a specific task, install a task, and segment an image with a task.

```bash
sct_deepseg -h
```

```bash
sct_deepseg spinalcord -h
```

```bash
sct_deepseg gm_mouse_t1 -install
```

```bash
sct_deepseg lesion_ms -i cMRI3712.nii.gz
```

--------------------------------

### Install a specific model version with -custom-url

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/lesion_ms_mp2rage.html

Example command to install a specific model version using the -custom-url option.

```bash
sct_deepseg lesion_ms_mp2rage -install -custom-url CUSTOM_URL
```

--------------------------------

### Run the SCT installation script

Source: https://spinalcordtoolbox.com/stable/user_section/installation/apptainer.html

Execute the installation script to set up the container. You can perform a basic installation or include specific DeepSeg tasks.

```bash
./install_sct_containered_{sct_version}.sh
```

```bash
./install_sct_containered_{sct_version}.sh spinalcord tumor_t2
```

--------------------------------

### Install X11 Utilities

Source: https://spinalcordtoolbox.com/stable/user_section/installation/linux.html

Install xauth and x11-xserver-utils on the host machine to support GUI redirection.

```bash
sudo apt install xauth x11-xserver-utils
```

--------------------------------

### Run SCT Installer Script

Source: https://spinalcordtoolbox.com/stable/user_section/installation/linux.html

Navigate to the download directory and execute the SCT installation script.

```bash
cd ~/Downloads
bash install_sct-<version>_linux.sh
```

--------------------------------

### Optional argument examples

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/sct_dmri_moco.html

Examples of file inputs for optional arguments.

```text
bvals.txt
```

```text
dmri_mask.nii.gz
```

--------------------------------

### Install SCT in Docker

Source: https://spinalcordtoolbox.com/stable/user_section/installation/linux.html

Commands to pull the Ubuntu image, install dependencies, clone the SCT repository, and install the toolbox.

```bash
sudo docker pull ubuntu:22.04
sudo docker run -it ubuntu:22.04
apt update
apt install git bzip2 curl gcc git libdbus-1-3 libgl1-mesa-glx libglib2.0-0 libxkbcommon-x11-0 libxrender1
git clone --branch 7.0 https://github.com/spinalcordtoolbox/spinalcordtoolbox.git sct
cd sct
./install_sct -iy
source /root/.bashrc
sct_testing
sudo docker ps -a
sudo docker commit <CONTAINER_ID> <IMAGE_NAME>/ubuntu:ubuntu22.04
```

--------------------------------

### Install Ubuntu via WSL

Source: https://spinalcordtoolbox.com/stable/user_section/installation/windows.html

Execute this command in an administrator PowerShell to install the default Ubuntu distribution.

```powershell
wsl --install
```

--------------------------------

### Install Spinal Cord Toolbox

Source: https://spinalcordtoolbox.com/stable/index.html

Execute the installation script on macOS or Linux systems.

```bash
./install_sct
```

--------------------------------

### batch_processing.sh source script

Source: https://spinalcordtoolbox.com/stable/user_section/getting-started.html

The full source of the batch_processing.sh script. It sets up environment variables, downloads example data, and runs the analysis. It includes options to prevent re-downloading (SCT_BP_DOWNLOAD=0), specify a QC folder (SCT_BP_QC_FOLDER), and skip QC removal (SCT_BP_NO_REMOVE_QC). The script aborts on error and installs the sct_deepseg model.

```bash
#!/bin/bash
#
# Example of commands to process multi-parametric data of the spinal cord.
#
# Please note that this batch script has a lot of redundancy and should not
# be used as a pipeline for regular processing. For example, there is no need
# to process both t1 and t2 to extract CSA values.
#
# For information about acquisition parameters, see: https://osf.io/wkdym/
# N.B. The parameters are set for these type of data. With your data, parameters
# might be slightly different.
#
# Usage:
#
#   [option] ./batch_processing.sh
#
#   Prevent (re-)downloading sct_example_data:
#   SCT_BP_DOWNLOAD=0 ./batch_processing.sh
#
#   Specify quality control (QC) folder (Default is ~/qc_batch_processing):
#   SCT_BP_QC_FOLDER=/user/toto/my_qc_folder ./batch_processing.sh

# Abort on error
set -ve

# For full verbose, uncomment the next line
# set -x

# Fetch OS type
if uname -a | grep -i  darwin > /dev/null 2>&1; then
  # OSX
  open_command="open"
elif uname -a | grep -i  linux > /dev/null 2>&1; then
  # Linux
  open_command="xdg-open"
fi

# Check if users wants to use his own data
if [[ -z "$SCT_BP_DOWNLOAD" ]]; then
	SCT_BP_DOWNLOAD=1
fi

# QC folder
if [[ -z "$SCT_BP_QC_FOLDER" ]]; then
	SCT_BP_QC_FOLDER=$(pwd)/"qc_example_data"
fi

# Remove QC folder
if [ -z "$SCT_BP_NO_REMOVE_QC" ] && [ -d "$SCT_BP_QC_FOLDER" ]; then
  echo "Removing $SCT_BP_QC_FOLDER folder."
  rm -rf "$SCT_BP_QC_FOLDER"
fi

# get starting time:
start=$(date +%s)

# download example data
if [[ "$SCT_BP_DOWNLOAD" == "1" ]]; then
  sct_download_data -d sct_example_data
fi

# Enter our data directory
cd "$SCT_DIR/data/sct_example_data"

# install the sct_deepseg model this script will use later
sct_deepseg spinalcord -install

```

--------------------------------

### Install sc_lumbar_t2 model

Source: https://spinalcordtoolbox.com/stable/user_section/tutorials/registration-to-template/lumbar-registration/lumbar-segmentation.html

Run this command to install the sc_lumbar_t2 model if it is not already installed.

```bash
sct_deepseg sc_lumbar_t2 -install

```

--------------------------------

### sct_deepseg gm_wm_exvivo_t2 usage help

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/gm_wm_exvivo_t2.html

Displays the command-line usage syntax and available arguments for the tool.

```bash
usage: sct_deepseg gm_wm_exvivo_t2 [-i <file> [<file> ...]] [-o <str>]
                                   [-install]
                                   [-custom-url CUSTOM_URL [CUSTOM_URL ...]]
                                   [-thr <float>] [-largest {0,1}]
                                   [-fill-holes {0,1}]
                                   [-remove-small REMOVE_SMALL [REMOVE_SMALL ...]]
                                   [-qc <folder>] [-qc-dataset <str>]
                                   [-qc-subject <str>] [-qc-plane <str>]
                                   [-qc-seg <file>] [-h] [-v <int>] [-r {0,1}]
```

--------------------------------

### Expected installation warnings

Source: https://spinalcordtoolbox.com/stable/user_section/installation/windows.html

These warnings are expected due to the lack of a default GUI environment in WSL.

```text
Check if figure can be opened with matplotlib.......[FAIL] (Using non-GUI backend 'agg')
Check if figure can be opened with PyQt.............[FAIL] ($DISPLAY not set on X11-supporting system)
```

--------------------------------

### Install NumPy

Source: https://spinalcordtoolbox.com/stable/user_section/installation/linux.html

Install the required numpy dependency.

```bash
pip install numpy
```

--------------------------------

### Display sct_register_multimodal help

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/all_tools.html

View the usage instructions and available arguments for the tool.

```bash
sct_register_multimodal -h
```

--------------------------------

### Mandatory argument examples

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/sct_dmri_moco.html

Examples of file inputs for mandatory arguments.

```text
dmri.nii.gz
```

```text
bvecs.txt
```

--------------------------------

### Install custom model with sct_deepseg spine

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/spine.html

Installs a specific version of a model by providing the URL to the .zip asset from the model's Releases page. Use with -install to install that version.

```bash
sct_deepseg spine -install -custom-url CUSTOM_URL
```

--------------------------------

### JSON configuration example for sct_run_batch

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/sct_run_batch.html

Example JSON configuration file for sct_run_batch. All arguments use underscores instead of dashes. The exclude_list can exclude entire subjects or individual sessions.

```json
{
    "path_data"   : "~/sct_data",
    "path_output" : "~/pipeline_results",
    "script"      : "nature_paper_analysis.sh",
    "jobs"        : -1,
    "exclude_list" : ["sub-01/ses-01", "sub-02", "ses-03"]
}

```

--------------------------------

### Install GCC via Homebrew

Source: https://spinalcordtoolbox.com/stable/user_section/installation/mac.html

Install GCC using Homebrew if it is not already present on your system.

```bash
brew install gcc
```
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