Last login: Mon Apr 15 15:46:56 on ttys000 The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://support.apple.com/kb/HT208050. (base) MacBook-Pro-de-Mathilde:~ mathilde$ softwareupdate --install-rosetta I have read and agree to the terms of the software license agreement. A list of Apple SLAs may be found here: https://www.apple.com/legal/sla/ Type A and press return to agree: A 2024-04-16 10:23:29.519 softwareupdate[2690:109067] Package Authoring Error: 042-78239: Package reference com.apple.pkg.RosettaUpdateAuto is missing installKBytes attribute Install of Rosetta 2 finished successfully (base) MacBook-Pro-de-Mathilde:~ mathilde$ gcc --version Apple clang version 15.0.0 (clang-1500.1.0.2.5) Target: arm64-apple-darwin23.3.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin (base) MacBook-Pro-de-Mathilde:~ mathilde$ gcc --version Apple clang version 15.0.0 (clang-1500.1.0.2.5) Target: arm64-apple-darwin23.3.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin (base) MacBook-Pro-de-Mathilde:~ mathilde$ sudo chown mathilde ~/.bash_profile Password: Sorry, try again. Password: (base) MacBook-Pro-de-Mathilde:~ mathilde$ ls Applications MSS1 Sites Desktop Movies anaconda3 Documents Music first pandas notebook.ipynb Downloads NetBeansProjects screen tp reseaux.pcapng GIT_FLOW Pictures spinalcordtoolbox GlassFish_Server Public Library README.md (base) MacBook-Pro-de-Mathilde:~ mathilde$ cd spinalcordtoolbox (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ sudo chown mathilde ~/.bashrc Password: chown: /Users/mathilde/.bashrc: No such file or directory (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ open ~/.bashrc The file /Users/mathilde/.bashrc does not exist. (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ ./install_sct ******************************* * Welcome to SCT installation * ******************************* Checking OS type and version... Darwin MacBook-Pro-de-Mathilde.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:30:27 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T8103 arm64 ProductVersion: 14.3 Checking requirements... OK! SCT version ......... 6.3.dev0 Installation type ... in-place Operating system .... osx ( 14.3) Shell config ........ /Users/mathilde/.bashrc SCT will be installed here: [/Users/mathilde/spinalcordtoolbox] Do you agree? [y]es/[n]o: y Skipping copy of source files (source and destination folders are the same) Removing sct and isct softlink from /Users/mathilde/spinalcordtoolbox/bin rm -rf /Users/mathilde/spinalcordtoolbox/python mkdir -p /Users/mathilde/spinalcordtoolbox/python rm -rf /Users/mathilde/spinalcordtoolbox/spinalcordtoolbox.egg-info Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y Downloading Miniconda... curl -sS -o /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/tmp.fvGSV2bpim/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh Installing Miniconda... bash /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/tmp.fvGSV2bpim/miniconda.sh -p /Users/mathilde/spinalcordtoolbox/python -b -f PREFIX=/Users/mathilde/spinalcordtoolbox/python Unpacking payload ... Installing base environment... Preparing transaction: ...working... done Executing transaction: ...working... done installation finished. Creating conda environment... Retrieving notices: ...working... done ERROR conda.notices.core:wrapper(123): Unable to open cache file: [Errno 13] Permission denied: '/Users/mathilde/Library/Caches/conda/notices/notices.cache' Channels: - defaults Platform: osx-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/mathilde/spinalcordtoolbox/python/envs/venv_sct added / updated specs: - python=3.9 The following packages will be downloaded: package | build ---------------------------|----------------- pip-23.3.1 | py39hecd8cb5_0 2.6 MB python-3.9.19 | h5ee71fb_0 12.7 MB setuptools-68.2.2 | py39hecd8cb5_0 950 KB wheel-0.41.2 | py39hecd8cb5_0 109 KB ------------------------------------------------------------ Total: 16.3 MB The following NEW packages will be INSTALLED: ca-certificates pkgs/main/osx-64::ca-certificates-2024.3.11-hecd8cb5_0 libcxx pkgs/main/osx-64::libcxx-14.0.6-h9765a3e_0 libffi pkgs/main/osx-64::libffi-3.4.4-hecd8cb5_0 ncurses pkgs/main/osx-64::ncurses-6.4-hcec6c5f_0 openssl pkgs/main/osx-64::openssl-3.0.13-hca72f7f_0 pip pkgs/main/osx-64::pip-23.3.1-py39hecd8cb5_0 python pkgs/main/osx-64::python-3.9.19-h5ee71fb_0 readline pkgs/main/osx-64::readline-8.2-hca72f7f_0 setuptools pkgs/main/osx-64::setuptools-68.2.2-py39hecd8cb5_0 sqlite pkgs/main/osx-64::sqlite-3.41.2-h6c40b1e_0 tk pkgs/main/osx-64::tk-8.6.12-h5d9f67b_0 tzdata pkgs/main/noarch::tzdata-2024a-h04d1e81_0 wheel pkgs/main/osx-64::wheel-0.41.2-py39hecd8cb5_0 xz pkgs/main/osx-64::xz-5.4.6-h6c40b1e_0 zlib pkgs/main/osx-64::zlib-1.2.13-h4dc903c_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done # # To activate this environment, use # # $ conda activate /Users/mathilde/spinalcordtoolbox/python/envs/venv_sct # # To deactivate an active environment, use # # $ conda deactivate Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1) Collecting pip!=21.2.* Using cached pip-24.0-py3-none-any.whl.metadata (3.6 kB) Using cached pip-24.0-py3-none-any.whl (2.1 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 23.3.1 Uninstalling pip-23.3.1: Successfully uninstalled pip-23.3.1 Successfully installed pip-24.0 Installing Python dependencies... Using requirements.txt (git installation) Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu Ignoring msvc-runtime: markers 'sys_platform == "win32"' don't match your environment Collecting certifi Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB) Collecting dipy!=1.6.*,!=1.7.*,!=1.8.* (from -r requirements.txt (line 7)) Using cached dipy-1.9.0-1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (9.0 kB) Collecting ivadomed (from -r requirements.txt (line 11)) Using cached ivadomed-2.9.10-py3-none-any.whl.metadata (6.4 kB) Collecting matplotlib (from -r requirements.txt (line 12)) Using cached matplotlib-3.8.4-cp39-cp39-macosx_10_12_x86_64.whl.metadata (5.8 kB) Collecting nibabel (from -r requirements.txt (line 21)) Using cached nibabel-5.2.1-py3-none-any.whl.metadata (8.8 kB) Collecting nilearn (from -r requirements.txt (line 22)) Downloading nilearn-0.10.4-py3-none-any.whl.metadata (7.8 kB) Collecting nnunetv2 (from -r requirements.txt (line 23)) 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(240 kB) Using cached shellingham-1.5.4-py2.py3-none-any.whl (9.8 kB) Using cached wrapt-1.16.0-cp39-cp39-macosx_10_9_x86_64.whl (37 kB) Using cached argparse-1.4.0-py2.py3-none-any.whl (23 kB) Using cached traceback2-1.4.0-py2.py3-none-any.whl (16 kB) Downloading typer-0.12.3-py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.2/47.2 kB 2.0 MB/s eta 0:00:00 Using cached markdown_it_py-3.0.0-py3-none-any.whl (87 kB) Using cached pygments-2.17.2-py3-none-any.whl (1.2 MB) Using cached smmap-5.0.1-py3-none-any.whl (24 kB) Using cached linecache2-1.0.0-py2.py3-none-any.whl (12 kB) Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB) Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, argparse, appdirs, zipp, xlsxwriter, wrapt, urllib3, typing-extensions, types-setuptools, transforms3d, traceback2, tqdm, tomli, threadpoolctl, tensorboard-data-server, sympy, sqlalchemy, smmap, six, shellingham, setuptools, setproctitle, pyyaml, python-gdcm, pyqt5-sip, pyparsing, pygments, pydicom, psutil, protobuf, portalocker, pluggy, pillow, packaging, ordered-set, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, click, charset-normalizer, certifi, bids-validator, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, tifffile, setuptools-scm, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, lazy_loader, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, deepdiff, csv-diff, contourpy, connected-components-3d, coloredlogs, trx-python, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dicom2nifti, wandb, typer, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, dipy, batchgenerators, pybids, neurite, acvl-utils, voxelmorph, torchio, nnunetv2, ivadomed Successfully installed Deprecated-1.2.14 GitPython-3.1.43 MarkupSafe-2.1.5 SimpleITK-2.3.1 absl-py-2.1.0 acvl-utils-0.2 appdirs-1.4.4 argparse-1.4.0 astor-0.8.1 batchgenerators-0.25 bids-validator-1.14.5 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 coloredlogs-15.0.1 connected-components-3d-3.14.1 contourpy-1.2.1 coverage-7.4.4 csv-diff-1.1 cycler-0.12.1 deepdiff-7.0.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.9.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.3.1 exceptiongroup-1.2.0 filelock-3.13.4 flatbuffers-24.3.25 fonttools-4.51.0 formulaic-0.3.4 fsspec-2024.3.1 future-1.0.0 gitdb-4.0.11 graphviz-0.20.3 grpcio-1.62.1 h5py-3.11.0 humanfriendly-10.0 humanize-4.9.0 idna-3.7 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.1.0 importlib-resources-6.4.0 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.10 jinja2-3.1.3 joblib-1.4.0 kiwisolver-1.4.5 lazy_loader-0.4 linecache2-1.0.0 loguru-0.7.2 lxml-5.2.1 markdown-3.6 markdown-it-py-3.0.0 matplotlib-3.8.4 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-5.2.1 nilearn-0.10.4 nnunetv2-2.3.1 num2words-0.5.13 numpy-1.23.5 onnx-1.16.0 onnxruntime-1.17.3 ordered-set-4.1.0 packaging-24.0 pandas-1.5.3 pillow-10.3.0 pluggy-1.4.0 portalocker-2.8.2 protobuf-4.25.3 psutil-5.9.8 pybids-0.15.5 pydicom-2.4.4 pygments-2.17.2 pyparsing-3.1.2 pyqt5-5.12.3 pyqt5-sip-12.12.2 pystrum-0.4 pytest-8.1.1 pytest-cov-5.0.0 pytest_console_scripts-1.4.1 python-dateutil-2.9.0.post0 python-gdcm-3.0.23.1 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.9.0 rich-13.7.1 scikit-image-0.22.0 scikit-learn-1.4.2 scipy-1.13.0 seaborn-0.13.2 sentry-sdk-1.45.0 setproctitle-1.3.3 setuptools-68.2.2 setuptools-scm-8.0.4 shellingham-1.5.4 six-1.16.0 smmap-5.0.1 sqlalchemy-1.3.24 sympy-1.12 tensorboard-2.16.2 tensorboard-data-server-0.7.2 threadpoolctl-3.4.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.2 torchio-0.19.6 torchvision-0.17.2 tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 trx-python-0.2.9 typer-0.12.3 types-setuptools-69.5.0.20240415 typing-extensions-4.11.0 unittest2-1.1.0 urllib3-2.2.1 voxelmorph-0.2 wandb-0.16.6 werkzeug-3.0.2 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.2.0 xlwt-1.3.0 yacs-0.1.8 zipp-3.18.1 Installing spinalcordtoolbox... Obtaining file:///Users/mathilde/spinalcordtoolbox Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Installing collected packages: spinalcordtoolbox Running setup.py develop for spinalcordtoolbox Successfully installed spinalcordtoolbox-6.3.dev0 Creating launchers for Python scripts... Installing binaries... sct_download_data -d binaries_osx -k -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d binaries_osx -k -- Trying URL: https://github.com/spinalcordtoolbox/spinalcordtoolbox-binaries/releases/download/r20221018/spinalcordtoolbox-binaries_osx.tar.gz Downloading: spinalcordtoolbox-binaries_osx.tar.gz Status: 100%|██████████| 65.3M/65.3M [00:06<00:00, 10.1MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-44-43_install-data_dd3s_7c3) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-44-43_install-data_dd3s_7c3 Copying data to: /Users/mathilde/spinalcordtoolbox/bin Updating existing '/Users/mathilde/spinalcordtoolbox/bin/isct_ComposeMultiTransform' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/isct_antsApplyTransforms' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/isct_antsRegistration' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/isct_antsSliceRegularizedRegistration' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/isct_dice_coefficient' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/isct_propseg' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/isct_spine_detect' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/isct_stitching' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/isct_train_svm' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/copyright/LICENSE_ANTs.txt' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/copyright/LICENSE_ctrDetect.txt' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/copyright/LICENSE_opencv.txt' Updating existing '/Users/mathilde/spinalcordtoolbox/bin/copyright/LICENSE_stitching.txt' Removing temporary folders... Done! All requirements installed! Installing data... mkdir -p /Users/mathilde/spinalcordtoolbox/data sct_download_data -d PAM50 -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d PAM50 -- Removing existing destination folder '/Users/mathilde/spinalcordtoolbox/data/PAM50' Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20240215/PAM50-r20240215.zip Downloading: PAM50-r20240215.zip Status: 100%|██████████| 104M/104M [00:09<00:00, 11.0MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-44-56_install-data_4pah8glk) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-44-56_install-data_4pah8glk Copying data to: /Users/mathilde/spinalcordtoolbox/data/PAM50 Removing temporary folders... Done! sct_download_data -d deepseg_sc_models -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d deepseg_sc_models -- Removing existing destination folder '/Users/mathilde/spinalcordtoolbox/data/deepseg_sc_models' Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20220325_deepseg_sc_models_onnx.zip Downloading: 20220325_deepseg_sc_models_onnx.zip Status: 100%|██████████| 19.5M/19.5M [00:01<00:00, 10.4MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-44-59_install-data_izi1h3ix) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-44-59_install-data_izi1h3ix Copying data to: /Users/mathilde/spinalcordtoolbox/data/deepseg_sc_models Removing temporary folders... Done! sct_download_data -d deepseg_gm_models -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d deepseg_gm_models -- Removing existing destination folder '/Users/mathilde/spinalcordtoolbox/data/deepseg_gm_models' Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20220325_deepseg_gm_models_onnx.zip Downloading: 20220325_deepseg_gm_models_onnx.zip Status: 100%|██████████| 2.24M/2.24M [00:00<00:00, 6.78MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-45-01_install-data_paa5xxf0) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-45-01_install-data_paa5xxf0 Copying data to: /Users/mathilde/spinalcordtoolbox/data/deepseg_gm_models Removing temporary folders... Done! sct_download_data -d deepseg_lesion_models -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d deepseg_lesion_models -- Removing existing destination folder '/Users/mathilde/spinalcordtoolbox/data/deepseg_lesion_models' Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20220325_deepseg_lesion_models_onnx.zip Downloading: 20220325_deepseg_lesion_models_onnx.zip Status: 100%|██████████| 5.35M/5.35M [00:00<00:00, 9.28MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-45-03_install-data_m8e2t6m1) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-45-03_install-data_m8e2t6m1 Copying data to: /Users/mathilde/spinalcordtoolbox/data/deepseg_lesion_models Removing temporary folders... Done! sct_download_data -d deepreg_models -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d deepreg_models -- Removing existing destination folder '/Users/mathilde/spinalcordtoolbox/data/deepreg_models' Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip Downloading: models.zip Status: 100%|██████████| 158M/158M [00:15<00:00, 10.4MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-45-20_install-data_46ctkc_u) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-45-20_install-data_46ctkc_u Copying data to: /Users/mathilde/spinalcordtoolbox/data/deepreg_models Removing temporary folders... Done! sct_download_data -d PAM50_normalized_metrics -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d PAM50_normalized_metrics -- Removing existing destination folder '/Users/mathilde/spinalcordtoolbox/data/PAM50_normalized_metrics' Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20230222.zip Downloading: PAM50-normalized-metrics-r20230222.zip Status: 6.92MB [00:00, 7.64MB/s] Creating temporary folder (/var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-45-24_install-data_f6raz9ao) Unzip data to: /var/folders/2s/fkwbjjc572xbdpfccg9nb5r00000gn/T/sct_2024-04-16_10-45-24_install-data_f6raz9ao Copying data to: /Users/mathilde/spinalcordtoolbox/data/PAM50_normalized_metrics Removing temporary folders... Done! Removing existing destination folder '/Users/mathilde/spinalcordtoolbox/data/deepseg_models/t2star_sc' Status: 100%|██████████| 18.0M/18.0M [00:01<00:00, 9.38MB/s] Validate installation... -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_check_dependencies -- SYSTEM INFORMATION ------------------ SCT info: - version: git-master-6962e03b5906ab3466e6e330438dbea58d949407 - path: /Users/mathilde/spinalcordtoolbox OS: osx (macOS-10.16-x86_64-i386-64bit) CPU cores: Available: 8, Used by ITK functions: 8 RAM: Total: 8192MB, Used: 907MB, Available: 603MB OPTIONAL DEPENDENCIES --------------------- Check FSLeyes version...............................[ ] (127, '/bin/sh: fsleyes: command not found') MANDATORY DEPENDENCIES ---------------------- Check Python executable.............................[OK] Using bundled python 3.9.19 (main, Mar 21 2024, 12:08:14) [Clang 14.0.6 ] at /Users/mathilde/spinalcordtoolbox/python/envs/venv_sct/bin/python Check if data are installed.........................[OK] Check if dipy is installed........................../Users/mathilde/spinalcordtoolbox/spinalcordtoolbox/scripts/sct_check_dependencies.py:157: UserWarning: Private repos not supported. Skipping. for req in requirements.parse(requirements_txt): [OK] (1.9.0) Check if ivadomed is installed......................[OK] (2.9.10) Check if matplotlib is installed....................[OK] (3.8.4) Check if monai is installed.........................[OK] (1.3.0) Check if nibabel is installed.......................[OK] (5.2.1) Check if nilearn is installed.......................[OK] (0.10.4) Check if nnunetv2 is installed......................[OK] Check if numpy is installed.........................[OK] (1.23.5) Check if onnxruntime is installed...................[OK] (1.17.3) Check if pandas is installed........................[OK] (1.5.3) Check if portalocker is installed...................[OK] (2.8.2) Check if psutil is installed........................[OK] (5.9.8) Check if pyqt5 (5.12.3) is installed................[OK] (5.12.3) Check if pyqt5-sip is installed.....................[OK] Check if pytest is installed........................[OK] (8.1.1) Check if pytest-cov is installed....................[OK] (5.0.0) Check if requests is installed......................[OK] (2.31.0) Check if requirements-parser is installed...........[OK] (0.9.0) Check if scipy is installed.........................[OK] (1.13.0) Check if scikit-image is installed..................[OK] (0.22.0) Check if scikit-learn is installed..................[OK] (1.4.2) Check if xlwt is installed..........................[OK] (1.3.0) Check if tqdm is installed..........................[OK] (4.66.2) Check if transforms3d is installed..................[OK] (0.4.1) Check if urllib3 is installed.......................[OK] (2.2.1) Check if pytest_console_scripts is installed........[OK] Check if pyyaml is installed........................[OK] (6.0.1) Check if voxelmorph is installed....................[OK] (0.2) Check if wquantiles is installed....................[OK] (0.4) Check if xlsxwriter is installed....................[OK] (3.2.0) Check if spinalcordtoolbox is installed.............[OK] Check ANTs compatibility with OS ...................[OK] Check PropSeg compatibility with OS ................[OK] Check if figure can be opened with PyQt.............[OK] Check if figure can be opened with matplotlib.......[OK] (Using GUI backend: 'QtAgg') Open a new Terminal window to load environment variables, or run: source /Users/mathilde/.bashrc Installation finished successfully! (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ sct_check_dependencies -bash: sct_check_dependencies: command not found (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$