### 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
```

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

### 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

```

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

### 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
```

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

### 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)
```

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

### 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
```

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

### Install GCC on Debian/Ubuntu

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

Install the GNU Compiler Collection using the apt package manager.

```bash
apt install gcc
```

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

### Install SCT with pip for user

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

Install SCT in-place using pip for the current user when not using a virtual environment.

```bash
pip install --user -e .
```

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

### Install system dependencies in Ubuntu

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

Update the package list and install required software packages for SCT.

```bash
sudo apt-get update && sudo apt-get upgrade -y
sudo apt-get -y install gcc unzip python3-pip python3 psmisc net-tools git gfortran libjpeg-dev
```

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

### Install NumPy

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

Install the required numpy dependency.

```bash
pip install numpy
```

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

### Install model with custom URL

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/gm_mouse_t1.html

Installs a specific version of a model by providing the URL of the .zip asset from the model's Releases page.

```bash
sct_deepseg gm_mouse_t1 -install -custom-url CUSTOM_URL
```

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

### YAML configuration example for sct_run_batch

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

Example YAML configuration file for sct_run_batch. All arguments use underscores instead of dashes. The exclude_list can exclude entire subjects or individual sessions. Quotes are optional for strings in YAML but omitting them may cause parse errors.

```yaml
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"]  # this will exclude ses-01 for sub-01, all sessions for sub-02 and ses-03 for all subjects

```

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

### Run the batch processing script

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

Launches the SCT batch processing example script, which downloads example data and runs a typical multi-parametric MRI analysis. The script is located at $SCT_DIR/batch_processing.sh.

```bash
$SCT_DIR/batch_processing.sh

```

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

### Install SCT in Ubuntu Docker Container

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

Commands to pull the Ubuntu image, install dependencies, clone the SCT repository, and commit the container state.

```bash
# Start from Powershell or the Command Prompt
docker pull ubuntu:22.04
# Launch interactive mode (command-line inside container)
docker run -it ubuntu:22.04
# Now, inside Docker container, install dependencies
apt update
apt install git bzip2 curl gcc git libdbus-1-3 libgl1-mesa-glx libglib2.0-0 libxkbcommon-x11-0 libxrender1
# Note for above: libdbus-1-3, libgl1-mesa-glx, libglib2.0-0, libxkbcommon-x11-0, libxrender1 are required by PyQt
# Install SCT (you can change 7.0 for the version of your choice)
git clone --branch 7.0 https://github.com/spinalcordtoolbox/spinalcordtoolbox.git sct
cd sct
./install_sct -iy
source /root/.bashrc
# Test SCT
sct_testing
# Save the state of the container as a docker image.
# Back on the Host machine, open a new terminal and run:
docker ps -a  # list all containers (to find out the container ID)
# specify the ID, and also choose a name to use for the docker image, such as "sct_v7.0"
docker commit <CONTAINER_ID> <IMAGE_NAME>/ubuntu:ubuntu22.04
```

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

### 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
```

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

### Install GCC on CentOS/RedHat

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

Install the GNU Compiler Collection using the yum package manager.

```bash
yum -y install gcc
```

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

### Example parameter configuration with centermassrot and columnwise algorithms

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

Shows a parameter string where the columnwise algorithm is applied after a translation and rotation using the centermassrot algorithm, both using the MeanSquares metric.

```text
-param step=1,type=seg,algo=centermassrot,metric=MeanSquares:
       step=2,type=seg,algo=columnwise,metric=MeanSquares
```

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

### 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 SCT via Pip

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

Install SCT in editable mode, either within a virtual environment or the base environment.

```bash
pip install -e .
```

```bash
pip install --user -e .
```

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

### Install DeepSeg tasks post-installation

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

Update an existing sct.sif file to include additional DeepSeg tasks by running the provided installation script.

```bash
./install_deepseg_task.sh spinalcord t2_tumor
```

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

### Example: segment a single image

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/gm_sc_7t_t2star.html

Example command that segments the input image t2.nii.gz using the gm_sc_7t_t2star model.

```bash
sct_deepseg gm_sc_7t_t2star -i t2.nii.gz
```

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

### List WSL distributions

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

Check the installed distributions and their current WSL version.

```powershell
wsl --list --verbose
```

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

### Custom step=1 parameters for -param argument

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

Recommended starting parameters for the -param argument when customizing step=1 for rootlet-based registration. Use these as a base and adjust as needed.

```text
step=1,type=rootlet,algo=bsplinesyn,metric=CC,iter=6x6x3,shrink=8x4x2,smooth=0x0x0,slicewise=0,deformation=0x0x1,gradStep=0.1
```

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

### Check SCT Dependencies

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

Verify that GUI dependencies like PyQT and matplotlib are correctly installed.

```bash
sct_check_dependencies
```

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

### Install SCT with pip in virtualenv

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

Install SCT in-place using pip when working within a virtual environment.

```bash
pip install -e .
```

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

### Navigate to dMRI data directory

Source: https://spinalcordtoolbox.com/stable/user_section/tutorials/diffusion-weighted-mri/before-starting.html

Navigate to the dMRI data directory before starting the tutorial. Replace {PATH_TO_DOWNLOADED_DATA} with the actual path to the downloaded data.

```bash
cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/dmri/

```

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

### Input data argument example

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

Example of the mandatory input data argument for the sct_fmri_moco command.

```text
fmri.nii.gz
```

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

### Install FSLeyes

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

Commands to create a conda environment for FSLeyes and create a symbolic link for global access.

```bash
source ${SCT_DIR}/python/etc/profile.d/conda.sh
conda create -c conda-forge -p ~/fsleyes_env fsleyes -y
sudo ln -s ~/fsleyes_env/bin/fsleyes /usr/local/bin/fsleyes
```

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

### Generate QC reports

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

Examples of generating QC reports for different SCT processing functions.

```bash
sct_qc -i t2.nii.gz -s t2_seg.nii.gz -p sct_deepseg_sc
sct_qc -i t2.nii.gz -s t2_pmj.nii.gz -p sct_detect_pmj
sct_qc -i t2.nii.gz -s t2_seg_labeled.nii.gz -p sct_label_vertebrae
sct_qc -i t2.nii.gz -s t2_seg.nii.gz -p sct_deepseg_sc -qc-dataset mydata -qc-subject sub-45
sct_qc -i t2.nii.gz -s t2_seg.nii.gz -d t2_lesion.nii.gz -p sct_deepseg_lesion -plane axial
```

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

### sct_label_utils -project-centerline example

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

Example command for projecting labels onto a spinal cord segmentation or centerline using -project-centerline.

```bash
sct_label_utils -i spinalcord.nii.gz -project-centerline labels.nii.gz
```

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

### Crop image using reference image

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

Example command using a reference image's dimensions to crop the input image.

```bash
sct_crop_image -i t2.nii.gz -ref mt1.nii.gz
```

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

### Check GCC version

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

Verify if the Gnu Compiler Collection is installed on your system.

```bash
gcc --version
```

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

### Source bashrc

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

Apply the environment changes after installation.

```bash
source ~/.bashrc
```

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

### Crop image using binary mask

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

Example command using a binary mask to define the cropping bounding box.

```bash
sct_crop_image -i t2.nii.gz -m mask.nii.gz
```

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

### Crop image with binary mask and margin

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

Example command using a binary mask with a margin of 5 voxels on each side in the x and y directions only.

```bash
sct_crop_image -i t2.nii.gz -m mask.nii.gz -dilate 5x5x0
```

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

### Install Rosetta 2 for Apple silicon

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

Run this command in Terminal to install Rosetta 2 if your Mac uses Apple silicon (M1, M2, M3, etc.).

```bash
softwareupdate --install-rosetta
```

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

### Example parameter configuration for multi-step registration

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

Shows a recommended multi-step registration parameter string combining segmentation-based and image-based steps with increasing transformation complexity. Uses MeanSquares metric for segmentations and Mutual Information (MI) for different contrasts.

```text
-param step=1,type=seg,algo=slicereg,metric=MeanSquares:
       step=2,type=seg,algo=affine,metric=MeanSquares,gradStep=0.2:
       step=3,type=im,algo=syn,metric=MI,iter=5,shrink=2
```

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

### Include subjects or sessions via -include-list

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

Examples of using the -include-list flag to specify subjects or sessions for processing.

```bash
-include-list sub-001 sub-002
```

```bash
-include-list sub-001/ses-01 ses-02
```

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

### Crop image by specifying min/max bounds

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

Example command cropping the image along specific dimensions using min/max bounds. Here, cropping occurs between x=5 and x=60, and between z=5 and z=zmax-1.

```bash
sct_crop_image -i t2.nii.gz -xmin 5 -xmax 60 -zmin 5 -zmax -2
```

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

### Segment an image with sct_deepseg lesion_ms_mp2rage

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

Example command to segment a single image file using the lesion_ms_mp2rage model.

```bash
sct_deepseg lesion_ms_mp2rage -i t2.nii.gz
```

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

### 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}]
```

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

### Crop image using GUI

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

Example command using the graphical user interface to crop an image. This method does not allow cropping along the right-left dimension.

```bash
sct_crop_image -i t2.nii.gz -g 1
```

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

### 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
```

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

### Navigate to the multi_subject directory

Source: https://spinalcordtoolbox.com/stable/user_section/tutorials/analysis-pipelines-with-sct/before-starting.html

Use this command in a terminal to change into the tutorial's working directory. Replace {PATH_TO_DOWNLOADED_DATA} with the actual path where you downloaded the data.

```bash
cd {PATH_TO_DOWNLOADED_DATA}/multi_subject

```

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

### Register template to subject with -ref subject

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

Use the -ref subject parameter to register the template to the subject, skipping the straightening procedure. This example includes custom -param settings for centermassrot and columnwise algorithms.

```bash
sct_register_to_template -i data.nii.gz -s data_seg.nii.gz -l data_labels.nii.gz -ref subject -param step=1,type=seg,algo=centermassrot,smooth=0:step=2,type=seg,algo=columnwise,smooth=0,smoothWarpXY=2

```

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

### Display sct_register_to_template help

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

Displays the usage and available arguments for the command.

```bash
sct_register_to_template -h
```

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

### sct_maths usage help

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

Displays the command-line usage, available flags, and options for the sct_maths tool.

```bash
usage: sct_maths -i <file> -o <file> [-volumewise {0,1}] [-add [...]]
                 [-sub  [...]] [-mul [...]] [-div  [...]] [-mean {x,y,z,t}]
                 [-rms {x,y,z,t}] [-std {x,y,z,t}] [-bin <float>]
                 [-slicewise-mean {0,1,2}] [-otsu <int>] [-adap <list>]
                 [-otsu-median <list>] [-percent <int>] [-thr <float>]
                 [-uthr <float>] [-dilate <int>] [-erode <int>]
                 [-shape {square,cube,disk,ball}] [-dim {0,1,2}]
                 [-smooth <list>] [-laplacian <list>] [-denoise DENOISE]
                 [-mi <file>] [-minorm <file>] [-corr <file>]
                 [-symmetrize {0,1,2}]
                 [-type {uint8,int16,int32,float32,complex64,float64,int8,uint16,uint32,int64,uint64}]
                 [-h] [-v <int>]
```

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

### Display sct_straighten_spinalcord help

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

Run the help command to view usage instructions and available arguments for the tool.

```bash
sct_straighten_spinalcord -h
```

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

### Verify GUI Dependencies

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

Commands to prepare the runtime directory and verify GUI dependencies within the container.

```bash
mkdir /tmp/runtime-root
sct_check_dependencies
```

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

### sct_resample usage help

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

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

```bash
usage: sct_resample -i <file> [-f <str>] [-mm <str>] [-vox <str>] [-ref <file>]
                    [-x {nn,linear,spline}] [-o <file>] [-h] [-v <int>]
```

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

### Navigate to fMRI data directory

Source: https://spinalcordtoolbox.com/stable/user_section/tutorials/processing-fmri-data/before-starting.html

Use this command to change into the fMRI data directory after downloading the tutorial data. Replace {PATH_TO_DOWNLOADED_DATA} with the actual path to the downloaded data.

```bash
cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/fmri/

```

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

### Command-line usage

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

Full usage statement for sct_register_to_template, showing all available options and arguments.

```bash
usage: sct_register_to_template -i <file> -s <file> [-s-template-id <int>]
                                [-l <file>] [-ldisc <file>] [-lspinal <file>]
                                [-lrootlet <file>] [-ofolder <folder>]
                                [-t <folder>] [-c {t1,t2,t2s}]
                                [-ref {template,subject}] [-param <list>]
                                [-centerline-algo {polyfit,bspline,linear,nurbs}]
                                [-centerline-smooth <int>] [-qc <folder>]
                                [-qc-dataset <str>] [-qc-subject <str>] [-h]
                                [-v <int>] [-r {0,1}]

```

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

### Navigate to the T2* data directory

Source: https://spinalcordtoolbox.com/stable/user_section/tutorials/gray-matter-segmentation/improving-registration-with-gm-seg/before-starting.html

Change the current working directory to the location of the T2* data files required for the tutorial.

```bash
cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2s/
```

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

### Run Docker with X11 Redirection

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

Command to launch the container with environment variables configured for GUI support.

```bash
docker run -it --rm -e DISPLAY=<IPv4_ADDRESS>:<DISPLAY_NUMBER> -e XDG_RUNTIME_DIR=/tmp/runtime-root <IMAGE_NAME>/ubuntu:ubuntu22.04
```

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

### sct_process_segmentation usage help

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

Displays the command-line usage syntax and available flags for sct_process_segmentation.

```bash
usage: sct_process_segmentation -i <file> [-o <file>] [-append <int>] [-z <str>]
                                [-perslice <int>] [-vert <str>]
                                [-vertfile <str>] [-discfile <str>]
                                [-perlevel <int>] [-angle-corr <int>]
                                [-centerline <str>]
                                [-centerline-algo {polyfit,bspline,linear,nurbs}]
                                [-centerline-smooth <int>]
                                [-centerline-exclude-missing <int>]
                                [-pmj <file>] [-pmj-distance <float>]
                                [-pmj-extent <float>] [-anat <file>]
                                [-normalize <list> [<list> ...]]
                                [-normalize-PAM50 <int>] [-qc <folder>]
                                [-qc-image <str>] [-qc-dataset <str>]
                                [-qc-subject <str>] [-h] [-v <int>] [-r {0,1}]
```

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

### sct_run_batch help command

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

Displays the usage information and available options for the sct_run_batch tool.

```bash
sct_run_batch -h
```

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

### Configure XQuartz for GUI Redirection

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

Command to allow X11 connections from the local host in XQuartz.

```bash
xhost + 127.0.0.1
```

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

### Open QC report on Linux

Source: https://spinalcordtoolbox.com/stable/overview/concepts/inspecting-results-qc-fsleyes.html

Sample terminal output on Linux showing the command to open the QC report in a browser.

```bash
# Sample output (Linux) after running the SCT script
Use the following command to see the results in a browser:
xdg-open "qc_folder/index.html"

```

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

### sct_deepseg tumor_t2

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/tumor_t2.html

Command-line tool for segmenting tumors in T2-weighted images. Supports multiple input files, model installation, and various post-processing options.

```APIDOC
## sct_deepseg tumor_t2

### Description
Segments tumors in T2-weighted MRI images using deep learning models. Supports multiple input files, model installation, and various post-processing options.

### Usage
```
sct_deepseg tumor_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}]
```

### Parameters

#### Input/Output
- **-i** (file) - Required - Image filename(s) to segment. If segmenting multiple files, separate filenames with a space.
- **-o** (str) - Optional - Output file name. The chosen filename will be used as a base name, and model-specific suffixes will be added to the end depending on the type of output (e.g. '_cord.nii.gz', '_gm.nii.gz', etc.).

#### Tasks
- **-install** (flag) - Optional - Install models that are required for specified task. Default: `False`.
- **-custom-url** (str) - Optional - URL(s) pointing to the `.zip` asset for a model release. This option can be used with `-install` to install a specific version of a model. To use this option, navigate to the 'Releases' page of the model, find release you wish to install, and right-click + copy the URL of the `.zip` listed under 'Assets'. Example: `sct_deepseg tumor_t2 -install -custom-url CUSTOM_URL` `sct_deepseg tumor_t2 -i t2.nii.gz`.

#### Parameters
- **-thr** (float) - Optional - Binarize segmentation with specified threshold. Set to 0 for no thresholding (i.e., soft segmentation). Default value is '[0.5, 0.5]', and was chosen by experimentation (more info at https://github.com/sct-pipeline/deepseg-threshold).
- **-largest** (int) - Optional - Possible choices: 0, 1. Keep the largest connected object from each output segmentation; if not set, all objects are kept. Default: `0`.
- **-fill-holes** (int) - Optional - Possible choices: 0, 1. If set, small holes in the segmentation will be filled in automatically. Default: `0`.
- **-remove-small** (str) - Optional - Minimal object size to keep with unit (mm3 or vox). A single value can be provided or one value per prediction class. Single value example: 1mm3, 5vox. Multiple values example: 10 20 10vox (remove objects smaller than 10 voxels for class 1 and 3, and smaller than 20 voxels for class 2).

#### Misc Arguments
- **-qc** (folder) - Optional - The path where the quality control generated content will be saved.
- **-qc-dataset** (str) - Optional - If provided, this string will be mentioned in the QC report as the dataset the process was run on.
- **-qc-subject** (str) - Optional - If provided, this string will be mentioned in the QC report as the subject the process was run on.
- **-qc-plane** (str) - Optional - Possible choices: Axial, Sagittal. Plane of the output QC. If Sagittal, it is highly recommended to provide the `-qc-seg` option, as it will ensure the output QC is cropped to a reasonable field of view. Default: `'Axial'`.
- **-qc-seg** (file) - Optional - Segmentation file to use for cropping the QC. This option is useful when you want to QC a region that is different from the output segmentation. For example, it might be useful to provide a dilated cord segmentation to expand the QC field of view. If `-qc-seg` is not provided, the default behavior will depend on the value of `-qc-plane`: 'Axial': Without '-qc-seg', a sensible crop radius between 15-40 vox will be automatically used, depending on the resolution and segmentation type. 'Sagittal': Without '-qc-seg', the full image will be displayed by default. (For very large images, this may cause a crash, so using `-qc-seg` is highly recommended.)
- **-v** (int) - Optional - Possible choices: 0, 1, 2. Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode. Default: `1`.
- **-r** (int) - Optional - Possible choices: 0, 1. Remove temporary files. Default: `1`.

### Example
```
sct_deepseg tumor_t2 -i t2.nii.gz
```
```

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

### Run Docker with X11 Forwarding

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

Launch the container with privileged access and X11 display forwarding enabled.

```bash
sudo docker run -it --rm --privileged -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix <IMAGE_NAME>/ubuntu:ubuntu22.04
```

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

### Process included files using bash syntax

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

Example of using bash conditional logic to process specific files when using the -include-yml flag.

```bash
# check if FILE_T2 is in the list of included files
FILE_T2="$SUBJECT"_T2w.nii.gz
if [[ " $INCLUDE_FILES " =~ " $FILE_T2 " ]]; then
    # process file only if it is included
    FILE_T2_SEG="$SUBJECT"_T2w_seg.nii.gz
    sct_deepseg spinalcord $FILE_T2 -o $FILE_T2_SEG
fi
```

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

### Register subject to template using default settings

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

Performs the standard registration process using the input image, segmentation, and labels.

```bash
sct_register_to_template -i data.nii.gz -s data_seg.nii.gz -l
data_labels.nii.gz
```

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

### Transform displacement field to FSL warps

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

Example syntax for converting SCT warping fields to FSL format and applying them using FSL's applywarp.

```bash
sct_image -i WARP_SRC2DEST -to-fsl IM_SRC (IM_DEST) -o WARP_FSL
```

```bash
applywarp -i IM_SRC -r IM_DEST -w WARP_FSL --abs -o IM_SRC2DEST
```

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

### Open Quality Control Report

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

Command to launch the Quality Control (QC) report index file in the default web browser.

```bash
echo "To open Quality Control (QC) report on a web-browser, run the following:"
echo "$open_command $SCT_BP_QC_FOLDER/index.html"
```

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

### Set WSL version to 1

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

Convert a specific distribution to WSL version 1. Replace 'Ubuntu' with your distribution name if different.

```powershell
wsl --set-version Ubuntu 1
```

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

### Display sct_qc help

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

Displays the help message and usage information for the sct_qc command.

```bash
sct_qc -h
```

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

### sct_dice_coefficient usage

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

Shows the command-line usage for sct_dice_coefficient, including all options. Note that indexing starts at 0, and using -1 for a size sets it to the full image extent.

```bash
usage: sct_dice_coefficient -i <file> -d <file> [-2d-slices {0,1,2}] [-b <list>]
                            [-bmax {0,1}] [-bzmax {0,1}] [-bin {0,1}] [-o <str>]
                            [-h] [-v <int>] [-r {0,1}]

```

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

### sct_dmri_separate_b0_and_dwi

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/sct_dmri_separate_b0_and_dwi.html

Command-line tool to separate b=0 and diffusion-weighted images from a diffusion dataset. Output files get suffixes _b0 and _dwi appended to the input file name.

```APIDOC
## sct_dmri_separate_b0_and_dwi

### Description
Separate b=0 and DW images from diffusion dataset. The output files will have a suffix (_b0 and _dwi) appended to the input file name.

### Usage
```
sct_dmri_separate_b0_and_dwi -i <file> -bvec <file> [-a {0,1}] [-bval <file>] [-bvalmin <float>] [-ofolder <folder>] [-h] [-v <int>] [-r {0,1}]
```

### Arguments

#### Mandatory Arguments
- **-i** (file) - Required - Diffusion data. Example: `dmri.nii.gz`
- **-bvec** (file) - Required - Bvecs file. Example: `bvecs.txt`

#### Optional Arguments
- **-a** (choice: 0, 1) - Optional - Average b=0 and DWI data. 0 = no, 1 = yes. Default: `1`
- **-bval** (file) - Optional - bvals file. Used to identify low b-values (in case different from 0). Example: `bvals.txt`. Default: `''`
- **-bvalmin** (float) - Optional - B-value threshold (in s/mm2) below which data is considered as b=0. Example: `50.0`
- **-ofolder** (folder) - Optional - Output folder. Default: `'.'`

#### Miscellaneous Arguments
- **-v** (choice: 0, 1, 2) - Optional - Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode. Default: `1`
- **-r** (choice: 0, 1) - Optional - Remove temporary files. Default: `1`

### Notes
- The output files will have suffixes `_b0` and `_dwi` appended to the input file name.
- Use `-h` to display help.
```

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

### sct_deepseg gm_mouse_t1

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/gm_mouse_t1.html

Command-line tool to segment gray matter in mouse T1-weighted images. It supports multiple input files, model installation, and various segmentation post-processing options.

```APIDOC
## sct_deepseg gm_mouse_t1

### Description
Segments gray matter in mouse T1-weighted images using deep learning models. Supports multiple input files, model installation, and various post-processing options.

### Usage
```
sct_deepseg gm_mouse_t1 [-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}]
```

### Parameters

#### Input/Output
- **-i** (file list) - Required - Image filename(s) to segment. If segmenting multiple files, separate filenames with a space.
- **-o** (string) - Optional - Output file name. The chosen filename will be used as a base name, and model-specific suffixes will be added to the end depending on the type of output (e.g., '_cord.nii.gz', '_gm.nii.gz', etc.).

#### Tasks
- **-install** (flag) - Optional - Install models that are required for specified task. Default: False.
- **-custom-url** (string list) - Optional - URL(s) pointing to the .zip asset for a model release. Can be used with -install to install a specific version of a model. Example: `sct_deepseg gm_mouse_t1 -install -custom-url CUSTOM_URL`

#### Parameters
- **-thr** (float) - Optional - Binarize segmentation with specified threshold. Set to 0 for no thresholding (i.e., soft segmentation). Default value is '[0.0]'.
- **-largest** (choice: 0, 1) - Optional - Keep the largest connected object from each output segmentation; if not set, all objects are kept. Default: 0.
- **-fill-holes** (choice: 0, 1) - Optional - If set, small holes in the segmentation will be filled in automatically. Default: 0.
- **-remove-small** (string list) - Optional - Minimal object size to keep with unit (mm3 or vox). A single value can be provided or one value per prediction class. Example: 1mm3, 5vox. Multiple values example: 10 20 10vox.

#### Misc Arguments
- **-qc** (folder) - Optional - The path where the quality control generated content will be saved.
- **-qc-dataset** (string) - Optional - If provided, this string will be mentioned in the QC report as the dataset the process was run on.
- **-qc-subject** (string) - Optional - If provided, this string will be mentioned in the QC report as the subject the process was run on.
- **-qc-plane** (choice: Axial, Sagittal) - Optional - Plane of the output QC. If Sagittal, it is highly recommended to provide the -qc-seg option. Default: 'Axial'.
- **-qc-seg** (file) - Optional - Segmentation file to use for cropping the QC. If not provided, default behavior depends on -qc-plane.
- **-v** (choice: 0, 1, 2) - Optional - Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode. Default: 1.
- **-r** (choice: 0, 1) - Optional - Remove temporary files. Default: 1.

### Examples
```
sct_deepseg gm_mouse_t1 -i t2.nii.gz
sct_deepseg gm_mouse_t1 -install -custom-url CUSTOM_URL
```

```

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

### sct_detect_compression usage syntax

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

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

```bash
usage: sct_detect_compression -s <file> -discfile <file> [-num-of-slices <int>]
                              [-angle-corr <int>] [-o <file>] [-h] [-v <int>]
```

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

### Check method information

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

Displays detailed information about the slice-wise regularized registration method.

```bash
isct_antsSliceRegularizedRegistration
```

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

### sct_deepseg sc_canal_t2

Source: https://spinalcordtoolbox.com/stable/user_section/command-line/deepseg/sc_canal_t2.html

Segments the spinal cord and canal from T2-weighted images. This command accepts input image filenames and various options to control segmentation, model installation, and quality control.

```APIDOC
## sct_deepseg sc_canal_t2

### Description
Segments the spinal cord and canal from T2-weighted images. The command accepts one or more input image filenames and provides options for model installation, segmentation post-processing, and quality control.

### Usage
```
sct_deepseg sc_canal_t2 [-i <file> [<file> ...]] [-o <str>] [-install]
                       [-custom-url CUSTOM_URL [CUSTOM_URL ...]]
                       [-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}]
                       [-test-time-aug]
```

### Parameters
#### Input/Output
- **-i** (file list) - Required - Image filename(s) to segment. If segmenting multiple files, separate filenames with a space.
- **-o** (str) - Optional - Output file name. The chosen filename will be used as a base name, and model-specific suffixes will be added to the end depending on the type of output (e.g., '_cord.nii.gz', '_gm.nii.gz', etc.).

#### Tasks
- **-install** (flag) - Optional - Install models that are required for specified task. Default: False.
- **-custom-url** (URL list) - Optional - URL(s) pointing to the `.zip` asset for a model release. This option can be used with `-install` to install a specific version of a model. To use this option, navigate to the 'Releases' page of the model, find the release you wish to install, and right-click + copy the URL of the `.zip` listed under 'Assets'. Example: `sct_deepseg sc_canal_t2 -install -custom-url CUSTOM_URL` `sct_deepseg sc_canal_t2 -i t2.nii.gz`.

#### Parameters
- **-largest** (int, choices: 0, 1) - Optional - Keep the largest connected object from each output segmentation; if not set, all objects are kept. Default: 0.
- **-fill-holes** (int, choices: 0, 1) - Optional - If set, small holes in the segmentation will be filled in automatically. Default: 0.
- **-remove-small** (string list) - Optional - Minimal object size to keep with unit (mm3 or vox). A single value can be provided or one value per prediction class. Single value example: 1mm3, 5vox. Multiple values example: 10 20 10vox (remove objects smaller than 10 voxels for class 1 and 3, and smaller than 20 voxels for class 2).
- **-test-time-aug** (flag) - Optional - Perform test-time augmentation (TTA) by flipping the input image along all axes and averaging the resulting predictions. Note: The time it takes to run the model will increase due to the additional predictions. Default: False.

#### Misc Arguments
- **-qc** (folder) - Optional - The path where the quality control generated content will be saved.
- **-qc-dataset** (str) - Optional - If provided, this string will be mentioned in the QC report as the dataset the process was run on.
- **-qc-subject** (str) - Optional - If provided, this string will be mentioned in the QC report as the subject the process was run on.
- **-qc-plane** (str, choices: Axial, Sagittal) - Optional - Plane of the output QC. If Sagittal, it is highly recommended to provide the `-qc-seg` option, as it will ensure the output QC is cropped to a reasonable field of view. Default: 'Axial'.
- **-qc-seg** (file) - Optional - Segmentation file to use for cropping the QC. This option is useful when you want to QC a region that is different from the output segmentation. For example, it might be useful to provide a dilated cord segmentation to expand the QC field of view. If `-qc-seg` is not provided, the default behavior will depend on the value of `-qc-plane`: 'Axial': Without '-qc-seg', a sensible crop radius between 15-40 vox will be automatically used, depending on the resolution and segmentation type. 'Sagittal': Without '-qc-seg', the full image will be displayed by default. (For very large images, this may cause a crash, so using `-qc-seg` is highly recommended.)
- **-v** (int, choices: 0, 1, 2) - Optional - Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode. Default: 1.
- **-r** (int, choices: 0, 1) - Optional - Remove temporary files. Default: 1.

### Examples
```
sct_deepseg sc_canal_t2 -i t2.nii.gz
```
```
sct_deepseg sc_canal_t2 -install -custom-url CUSTOM_URL
```
```