SCT: Spinal Cord Toolbox
Spinal Cord Toolbox (SCT), a comprehensive software dedicated to the processing of spinal cord MRI data. SCT builds on previously-validated methods and includes state-ofthe-art MRI templates and atlases of the spinal cord, algorithms to segment and register new data to the templates, and motion correction methods for diffusion and functional time series.
References:
- Benjamin De Leenera, Simon Lévya, Sara M. Duponta, Vladimir S. Fonovc, Nikola Stikova,
D.Louis Collinsc, Virginie Callote, Julien Cohen-Adada
SCT: Spinal Cord Toolbox, an open-source software for processing spinal
cord MRI data
NeuroImage Volume 145, Part A, 15 January 2017, Pages 24-43. http://dx.doi.org/10.1016/j.neuroimage.2016.10.009
Documentation
Important Notes
- Module Name: SCT (see the modules page for more information)
- Unusual environment variables set
- SCT_HOME installation directory
- SCT_BIN executable directory
- SCT_DIR source code directory
- SCT_DATA sample data directory
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive [user@cn3104 ~]$ module load sct [+] Loading gcc 6.4.0 ... [+] Loading boost libraries v 5.11.3 ... [+] Loading SCT 4.3 ... [user@cn3104 ~]$ sct_check_dependencies -- Spinal Cord Toolbox (4.3) SCT info: - version: 4.3 - path: /usr/local/apps/SCT/4.3/src OS: linux (Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-centos-7.5.1804-Core) CPU cores: Available: 56, Used by SCT: 56 RAM: MemTotal: 263836448 kB total used free shared buff/cache available Mem: 257652 26782 97522 1 133348 229743 Swap: 2047 24 2023 Check Python executable.............................[OK] Using bundled python 3.6.10 |Anaconda, Inc.| (default, May 8 2020, 02:54:21) [GCC 7.3.0] at /usr/local/apps/SCT/4.3/src/python/envs/venv_sct/bin/python Check if data are installed.........................[OK] Check if numpy is installed.........................[OK] (1.18.5) Check if colored is installed.......................[OK] (1.4.2) Check if dipy is installed..........................[OK] (1.1.1) Check if futures is installed.......................[OK] Check if h5py is installed..........................[OK] (2.10.0) Check if ivadomed (1.2.1) is installed..............[OK] (1.2.1) Check if Keras (2.1.5) is installed.................[OK] (2.1.5) Check if matplotlib is installed....................[OK] (3.2.1) Check if nibabel is installed.......................[OK] (3.1.0) Check if pandas is installed........................[OK] (1.0.4) Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3) Check if pytest is installed........................[OK] (5.4.3) Check if pytest-cov is installed....................[OK] (2.9.0) Check if raven is installed.........................[OK] Check if requests is installed......................[OK] (2.23.0) Check if requirements-parser is installed...........[OK] (0.2.0) Check if scipy is installed.........................[OK] (1.4.1) Check if scikit-image is installed..................[OK] (0.17.2) Check if scikit-learn is installed..................[OK] (0.23.1) Check if tensorflow (1.5.0) is installed............[OK] (1.5.0) Check if torch (1.5.0+cpu) is installed.............[OK] (1.5.0+cpu) Check if torchvision (0.6.0+cpu) is installed.......[OK] (0.6.0+cpu) Check if xlwt is installed..........................[OK] (1.3.0) Check if tqdm is installed..........................[OK] (4.46.1) Check if transforms3d is installed..................[OK] (0.3.1) Check if urllib3 is installed.......................[OK] (1.25.9) Check if spinalcordtoolbox is installed.............[OK] Check ANTs compatibility with OS ...................[OK] Check PropSeg compatibility with OS ................[OK] Check if DISPLAY variable is set....................[OK] ...Other executables sct_* available with the SCT can be listed by typing the command:
[user@cn3104 ~]$ ls $SCT_BINTo get started, run the command:
[user@cn3104 ~]$ $SCT_DIR/batch_processing.sh ... -- Spinal Cord Toolbox (4.3) Trying URL: https://osf.io/kjcgs/?action=download Downloading: 20180525_sct_example_data.zip Status: 100%|██████████████████████████████████████████████████████| 44.3M/44.3M [00:01<00:00, 22.4MB/s] Creating temporary folder (/tmp/sct-20200803173828.633996-djib9nx6) Unzip data to: /tmp/sct-20200803173828.633996-djib9nx6 Destination folder: /usr/local/apps/SCT/4.3 Checking if folder already exists... Removing temporary folders... Done! ... Look for template... Path template: /usr/local/apps/SCT/4.3/src/data/PAM50 Open template and vertebral levels... Disc values from template: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] Z-values for each disc: [962, 939, 908, 871, 834, 801, 770, 736, 693, 647, 601, 552, 501, 450, 397, 343, 290, 232, 169, 106, 56] Distances between discs (in voxel): [23.0, 31.0, 37.0, 37.0, 33.0, 31.0, 34.0, 43.0, 46.0, 46.0, 49.0, 51.0, 51.0, 53.0, 54.0, 53.0, 58.0, 63.0, 63.0, 50.0] Detect intervertebral discs... Current disc: 2 (z=308). Direction: superior .. Peak found: z=-1 (correlation = 0.5896971970624495) Current disc: 1 (z=338). Direction: superior .. correcting factor: 1.0 .. Switching to inferior direction. Current disc: 3 (z=271). Direction: inferior .. Peak found: z=-1 (correlation = 0.4784965058404901) .. correcting factor: 1.0 ... Generate output files... File created: ./t2_seg_labeled.nii.gz File created: ./t2_seg_labeled_discs.nii.gz File created: ./warp_curve2straight.nii.gz File created: ./warp_straight2curve.nii.gz File created: ./straight_ref.nii.gz ... # Display results (to easily compare integrity across SCT versions) # =========================================================================================== set +v **4.3** ~~ Ran on: Linux cn3146 3.10.0-862.14.4.el7.x86_64 Duration: 0hrs 33min 6sec --- t2/CSA: 73.87711295363036 mt/MTR(WM): 54.418871068394935 t2s/CSA_GM: 12.487834828856178 t2s/CSA_WM: 64.93830702088246 dmri/FA(CST_r): 0.7756557415994955 dmri/FA(CST_l): 0.7801552123851562 ~~ To open Quality Control (QC) report on a web-browser, run the following: xdg-open /usr/local/apps/SCT/4.3/qc_example_data/index.htmlEnd the interactive session:
[user@cn3104 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$