.. _command-line-tools:
Command-Line Tools
##################
Summary of 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".
Segmentation
============
- sct_create_mask_ - Create mask along z direction.
- sct_deepseg_ - Segment an anatomical structure or pathologies according using a deep learning model created with `ivadomed `_.
- sct_deepseg_gm_ - Segment spinal cord gray matter using deep learning.
- sct_deepseg_lesion_ - Segment multiple sclerosis lesions.
- sct_deepseg_sc_ - Segment spinal cord using deep learning.
- sct_get_centerline_ - Extracts the spinal cord centerline.
- sct_propseg_ - Segment spinal cord using propagation of deformation model (PropSeg).
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_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.
Main Tools
**********
sct_analyze_lesion
==================
.. program-output:: sct_analyze_lesion -h
sct_analyze_texture
===================
.. program-output:: sct_analyze_texture -h
sct_apply_transfo
=================
.. program-output:: sct_apply_transfo -h
sct_compute_ernst_angle
=======================
.. program-output:: sct_compute_ernst_angle -h
sct_compute_hausdorff_distance
==============================
.. program-output:: sct_compute_hausdorff_distance -h
sct_compute_compression
=======================
.. program-output:: sct_compute_compression -h
sct_compute_mtr
===============
.. program-output:: sct_compute_mtr -h
sct_compute_mtsat
=================
.. program-output:: sct_compute_mtsat -h
sct_compute_snr
===============
.. program-output:: sct_compute_snr -h
sct_convert
==============
.. program-output:: sct_convert -h
sct_create_mask
===============
.. program-output:: sct_create_mask -h
sct_crop_image
==============
.. program-output:: sct_crop_image -h
sct_deepseg
===========
.. program-output:: sct_deepseg -h
sct_deepseg_gm
==============
.. program-output:: sct_deepseg_gm -h
sct_deepseg_lesion
==================
.. program-output:: sct_deepseg_lesion -h
sct_deepseg_sc
==============
.. program-output:: sct_deepseg_sc -h
sct_denoising_onlm
==================
.. program-output:: sct_denoising_onlm -h
sct_detect_pmj
==============
.. program-output:: sct_detect_pmj -h
sct_dice_coefficient
====================
.. program-output:: sct_dice_coefficient -h
sct_dmri_compute_bvalue
=======================
.. program-output:: sct_dmri_compute_bvalue -h
sct_dmri_compute_dti
====================
.. program-output:: sct_dmri_compute_dti -h
sct_dmri_concat_bvals
=====================
.. program-output:: sct_dmri_concat_bvals -h
sct_dmri_concat_bvecs
=====================
.. program-output:: sct_dmri_concat_bvecs -h
sct_dmri_denoise_patch2self
===========================
.. program-output:: sct_dmri_denoise_patch2self -h
sct_dmri_display_bvecs
======================
.. program-output:: sct_dmri_display_bvecs -h
sct_dmri_moco
=============
.. program-output:: sct_dmri_moco -h
sct_dmri_separate_b0_and_dwi
============================
.. image:: https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/command-line/sct_dmri_separate_b0_and_dwi_example.png
.. program-output:: sct_dmri_separate_b0_and_dwi -h
sct_dmri_transpose_bvecs
========================
.. program-output:: sct_dmri_transpose_bvecs -h
sct_download_data
=================
.. program-output:: sct_download_data -h
sct_extract_metric
==================
.. program-output:: sct_extract_metric -h
sct_flatten_sagittal
====================
.. program-output:: sct_flatten_sagittal -h
sct_fmri_compute_tsnr
=====================
.. program-output:: sct_fmri_compute_tsnr -h
sct_fmri_moco
=============
.. program-output:: sct_fmri_moco -h
sct_get_centerline
==================
.. program-output:: sct_get_centerline -h
sct_image
=========
.. program-output:: sct_image -h
sct_label_utils
===============
.. program-output:: sct_label_utils -h
sct_label_vertebrae
===================
.. program-output:: sct_label_vertebrae -h
sct_maths
=========
.. program-output:: sct_maths -h
sct_merge_images
================
.. program-output:: sct_merge_images -h
sct_process_segmentation
========================
.. program-output:: sct_process_segmentation -h
sct_propseg
===========
.. image:: https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/command-line/sct_propseg_example.png
.. program-output:: sct_propseg -h
sct_qc
======
.. program-output:: sct_qc -h
sct_register_multimodal
=======================
.. program-output:: sct_register_multimodal -h
sct_register_to_template
========================
.. program-output:: sct_register_to_template -h
sct_resample
============
.. program-output:: sct_resample -h
sct_run_batch
=============
.. program-output:: sct_run_batch -h
sct_smooth_spinalcord
=====================
.. program-output:: sct_smooth_spinalcord -h
sct_straighten_spinalcord
=========================
.. program-output:: sct_straighten_spinalcord -h
sct_warp_template
=================
.. program-output:: sct_warp_template -h
System Commands
***************
sct_check_dependencies
======================
.. program-output:: sct_check_dependencies -h
sct_version
===========
.. program-output:: sct_version