Command-Line Tools

The command-line tools are named sct_*; to see all the commands available from SCT, start a new Terminal and type sct then press “tab”.

Each command-line tool has a dedicated documentation page where you will find its “help text”, with each page linked below. To quickly search the help text of all of the tools at once, please navigate to the Help text (-h) for all tools page and type Ctrl+F to search.

Segmentation

• sct_create_mask - Create mask along z direction.

• sct_deepseg - Segment anatomical structures or pathologies using deep learning models created with different frameworks (ivadomed, nnUNet, monai).

• sct_deepseg_gm - Segment spinal cord gray matter using deep learning.

• sct_get_centerline - Extracts the spinal cord centerline.

• sct_propseg - Segment spinal cord using propagation of deformation model (PropSeg).

• sct_deepseg_sc - Segment spinal cord using deep learning. [DEPRECATED] Please use sct_deepseg spinalcord instead.

• sct_deepseg_lesion - Segment multiple sclerosis lesions. [DEPRECATED] Please use sct_deepseg ms_lesion instead.

Segmentation Analysis

• sct_analyze_lesion - Compute statistics on segmented lesions.

• sct_compute_hausdorff_distance - Compute the Hausdorff’s distance between two binary images.

• sct_compute_compression - Compute spinal cord compression morphometrics.

• sct_detect_compression - Predict compression probability using spinal cord morphometrics.

• sct_dice_coefficient - Compute the Dice Coefficient to estimate overlap between two binary images.

• sct_process_segmentation - Perform various types of processing from the spinal cord segmentation.

Labeling

• sct_detect_pmj - Detection of the Ponto-Medullary Junction (PMJ).

• sct_label_vertebrae - Label vertebral levels

• sct_label_utils - Collection of tools to create or process labels

Registration

• sct_apply_transfo - Apply transformations.

• sct_get_centerline - Reconstruct spinal cord centerline.

• sct_register_multimodal - Register two images together (non-linear, constrained in axial plane)

• sct_register_to_template - Register an image with an anatomical template (eg. the PAM50 template).

• sct_straighten_spinalcord - Straighten spinal cord from centerline

• sct_warp_template - Warps the template and all atlases to a destination image.

Diffusion MRI

• sct_dmri_compute_bvalue - Calculate b-value (in mm^2/s).

• sct_dmri_concat_bvals - Concatenate bval files in time.

• sct_dmri_concat_bvecs - Concatenate bvec files in time.

• sct_dmri_compute_dti - Compute Diffusion Tensor Images (DTI) using dipy.

• sct_dmri_denoise_patch2self - Denoise images using dipy.

• sct_dmri_display_bvecs - Display scatter plot of gradient directions from bvecs file.

• sct_dmri_moco - Slice-wise motion correction of DWI data.

• sct_dmri_separate_b0_and_dwi - Separate b=0 and DW images from diffusion dataset.

• sct_dmri_transpose_bvecs - Transpose bvecs file.

Magnetization transfer

• sct_compute_mtr - Compute magnetization transfer ratio (MTR).

• sct_compute_mtsat - Compute MTsat and T1map [Helms et al. Magn Reson Med 2008].

Functional MRI

• sct_fmri_compute_tsnr - Compute the temporal signal-to-noise ratio from fMRI nifti files.

• sct_fmri_moco - Correct fMRI data for motion.

Metric processing

• sct_analyze_texture - Extraction of grey level co-occurence matrix (GLCM) texture features from an image within a given mask.

• sct_extract_metric - Estimate metric value within tracts, taking into account partial volume effect.

Image manipulation

• sct_convert - Convert image file to another type.

• sct_crop_image - Tools to crop an image, either via command line or via a Graphical User Interface (GUI).

• sct_denoising_onlm - Utility function to denoise images.

• sct_flatten_sagittal - Flatten the spinal cord in the sagittal plane (to make nice pictures).

• sct_image - Performs various operations on images (split, pad, etc.).

• sct_maths - Performs mathematical operations on images (threshold, smooth, etc.).

• sct_merge_images - Merge images to the same space.

• sct_resample - Anisotropic resampling of 3D or 4D data.

• sct_smooth_spinalcord - Smooth the spinal cord along its centerline.

Miscellaneous

• sct_compute_ernst_angle - Compute Ernst angle.

• sct_compute_snr - Compute SNR using methods described in [Dietrich et al. JMRI 2007].

• sct_download_data - Download binaries from the web.

• sct_qc - Generate Quality Control (QC) report following SCT processing.

• sct_run_batch - Wrapper to processing scripts, which loops across subjects.

System tools

• sct_check_dependencies - Check installation and compatibility of SCT.

• sct_version - Display SCT version.