Last login: Tue Feb 27 20:45:34 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 2024-02-28 00:06:39.255 softwareupdate[68221:4455566] 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$ ls -lah ~/ | grep bash_profile -rw-r--r-- 1 root staff 463B 7 fév 15:46 .bash_profile (base) MacBook-Pro-de-Mathilde:~ mathilde$ chmod +r ~/.bash_profile (base) MacBook-Pro-de-Mathilde:Downloads mathilde$ bash install_sct-6.2_macos.sh bash: install_sct-6.2_macos.sh: Operation not permitted (base) MacBook-Pro-de-Mathilde:Downloads mathilde$ git clone https://github.com/spinalcordtoolbox/spinalcordtoolbox fatal: destination path 'spinalcordtoolbox' already exists and is not an empty directory. (base) MacBook-Pro-de-Mathilde:Downloads mathilde$ cd spinalcordtoolbox (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 ./install_sct: line 273: /Users/mathilde/.bash_profile: Permission denied Installation failed! Please find the file "/Users/mathilde/Downloads/spinalcordtoolbox/install_sct_log.txt", then upload it as a .txt attachment in a new topic on SCT's forum: --> http://forum.spinalcordmri.org/c/sct (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ ls -lah ~/ | grep bash_profile -rw-r--r-- 1 root staff 463B 7 fév 15:46 .bash_profile (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ chmod +r ~/.bash_profile (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ ls -lah ~/ | grep bash_profile -rw-r--r-- 1 root staff 463B 7 fév 15:46 .bash_profile (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 ./install_sct: line 273: /Users/mathilde/.bash_profile: Permission denied Installation failed! Please find the file "/Users/mathilde/Downloads/spinalcordtoolbox/install_sct_log.txt", then upload it as a .txt attachment in a new topic on SCT's forum: --> http://forum.spinalcordmri.org/c/sct (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ chmod 777 ~/.bash_profile chmod: Unable to change file mode on /Users/mathilde/.bash_profile: Operation not permitted (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 ./install_sct: line 273: /Users/mathilde/.bash_profile: Permission denied Installation failed! Please find the file "/Users/mathilde/Downloads/spinalcordtoolbox/install_sct_log.txt", then upload it as a .txt attachment in a new topic on SCT's forum: --> http://forum.spinalcordmri.org/c/sct (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ chmod 000 .bash_profile_permission chmod: .bash_profile_permission: No such file or directory (base) MacBook-Pro-de-Mathilde:spinalcordtoolbox mathilde$ sudo ./install_sct Password: ******************************* * 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/Downloads/spinalcordtoolbox] Do you agree? [y]es/[n]o: y Skipping copy of source files (source and destination folders are the same) Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y Downloading Miniconda... curl -sS -o /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.qBd9EVZPmD/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh Installing Miniconda... bash /var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.qBd9EVZPmD/miniconda.sh -p /Users/mathilde/Downloads/spinalcordtoolbox/python -b -f PREFIX=/Users/mathilde/Downloads/spinalcordtoolbox/python Unpacking payload ... Extracting : platformdirs-3.10.0-py312hecd8cb5_0.conda: 3%|▎ | 2/69 [00:00<00:13, 5.14Extracting : openssl-3.0.13-hca72f7f_0.conda: 4%|▍ | 3/69 [00:00<00:12, 5.14it/s] Extracting : setuptools-68.2.2-py312hecd8cb5_0.conda: 7%|▋ | 5/69 [00:00<00:04, 14.36itExtracting : setuptools-68.2.2-py312hecd8cb5_0.conda: 9%|▊ | 6/69 [00:00<00:04, 15.27itExtracting : readline-8.2-hca72f7f_0.conda: 9%|▊ | 6/69 [00:00<00:04, 15.27it/s] Extracting : conda-content-trust-0.2.0-py312hecd8cb5_0.conda: 10%|█ | 7/69 [00:00<00:04,Extracting : pluggy-1.0.0-py312hecd8cb5_1.conda: 12%|█▏ | 8/69 [00:00<00:03, 15.27it/s] Extracting : requests-2.31.0-py312hecd8cb5_1.conda: 16%|█▌ | 11/69 [00:00<00:03, 15.27it/Extracting : ca-certificates-2023.12.12-hecd8cb5_0.conda: 17%|█▋ | 12/69 [00:00<00:03, 15Extracting : pip-23.3.1-py312hecd8cb5_0.conda: 19%|█▉ | 13/69 [00:00<00:03, 15.27it/s] Extracting : truststore-0.8.0-py312hecd8cb5_0.conda: 32%|███▏ | 22/69 [00:01<00:04, 11.56itExtracting : wheel-0.41.2-py312hecd8cb5_0.conda: 33%|███▎ | 23/69 [00:01<00:03, 11.56it/s] Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda: 36%|███▌ | 25/69 [00:01<00:03, 11Extracting : pybind11-abi-4-hd3eb1b0_1.conda: 38%|███▊ | 26/69 [00:01<00:03, 11.56it/s] Extracting : libedit-3.1.20230828-h6c40b1e_0.conda: 39%|███▉ | 27/69 [00:01<00:03, 11.56it/Extracting : brotli-python-1.0.9-py312hcec6c5f_7.conda: 41%|████ | 28/69 [00:01<00:03, 11.5Extracting : zstd-1.5.5-hc035e20_0.conda: 42%|████▏ | 29/69 [00:01<00:03, 11.56it/s] Extracting : cryptography-41.0.7-py312h30e54ef_0.conda: 45%|████▍ | 31/69 [00:01<00:03, 11.5Extracting : pycosat-0.6.6-py312h6c40b1e_0.conda: 46%|████▋ | 32/69 [00:01<00:03, 11.56it/s]Extracting : packaging-23.1-py312hecd8cb5_0.conda: 48%|████▊ | 33/69 [00:01<00:03, 11.56it/sExtracting : libarchive-3.6.2-h29ab7a1_2.conda: 49%|████▉ | 34/69 [00:01<00:03, 11.56it/s] Extracting : conda-libmamba-solver-23.12.0-pyhd3eb1b0_1.conda: 54%|█████▎ | 37/69 [00:01<00:0Extracting : bzip2-1.0.8-h1de35cc_0.conda: 55%|█████▌ | 38/69 [00:01<00:02, 11.56it/s] Extracting : conda-package-handling-2.2.0-py312hecd8cb5_0.conda: 59%|█████▉ | 41/69 [00:01<00Extracting : c-ares-1.19.1-h6c40b1e_0.conda: 61%|██████ | 42/69 [00:01<00:02, 11.56it/s] Extracting : ruamel.yaml-0.17.21-py312h6c40b1e_0.conda: 70%|██████▉ | 48/69 [00:01<00:00, 41.9Extracting : libmamba-1.5.3-h63cd6dc_0.conda: 71%|███████ | 49/69 [00:01<00:00, 41.98it/s] Extracting : libmambapy-1.5.3-py312h8c3233a_0.conda: 72%|███████▏ | 50/69 [00:01<00:00, 41.98itExtracting : jsonpointer-2.1-pyhd3eb1b0_0.conda: 74%|███████▍ | 51/69 [00:01<00:00, 41.98it/s] Extracting : zstandard-0.19.0-py312h6c40b1e_0.conda: 88%|████████▊ | 61/69 [00:02<00:00, 53.39itExtracting : conda-package-streaming-0.9.0-py312hecd8cb5_0.conda: 90%|████████▉ | 62/69 [00:02<0Extracting : libiconv-1.16-hca72f7f_2.conda: 91%|█████████▏| 63/69 [00:02<00:00, 53.39it/s] Extracting : certifi-2024.2.2-py312hecd8cb5_0.conda: 96%|█████████▌| 66/69 [00:02<00:00, 27.77itExtracting : lz4-c-1.9.4-hcec6c5f_0.conda: 97%|█████████▋| 67/69 [00:02<00:00, 27.77it/s] Installing base environment... Downloading and Extracting Packages: ...working... done Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Executing transaction: ...working... done installation finished. Creating conda environment... Channels: - defaults Platform: osx-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/mathilde/Downloads/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-3.9.18 | h5ee71fb_0 12.7 MB setuptools-68.2.2 | py39hecd8cb5_0 950 KB tzdata-2024a | h04d1e81_0 116 KB wheel-0.41.2 | py39hecd8cb5_0 109 KB xz-5.4.6 | h6c40b1e_0 373 KB ------------------------------------------------------------ Total: 16.8 MB The following NEW packages will be INSTALLED: ca-certificates pkgs/main/osx-64::ca-certificates-2023.12.12-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-3.9.18-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/Downloads/spinalcordtoolbox/python/envs/venv_sct # # To deactivate an active environment, use # # $ conda deactivate WARNING: The directory '/Users/mathilde/Library/Caches/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag. Requirement already satisfied: pip!=21.2.* in ./python/envs/venv_sct/lib/python3.9/site-packages (23.3.1) Collecting pip!=21.2.* Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB) Downloading pip-24.0-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 4.2 MB/s eta 0:00:00 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 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv Installing Python dependencies... Using requirements.txt (git installation) WARNING: The directory '/Users/mathilde/Library/Caches/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag. 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 Downloading 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)) Downloading dipy-1.5.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (3.9 kB) Collecting ivadomed (from -r requirements.txt (line 11)) Downloading ivadomed-2.9.9-py3-none-any.whl.metadata (6.5 kB) Collecting matplotlib (from -r requirements.txt (line 12)) Downloading matplotlib-3.8.3-cp39-cp39-macosx_10_12_x86_64.whl.metadata (5.8 kB) Collecting nibabel (from -r requirements.txt (line 21)) Downloading nibabel-5.2.1-py3-none-any.whl.metadata (8.8 kB) Collecting nilearn (from -r requirements.txt (line 22)) Downloading nilearn-0.10.3-py3-none-any.whl.metadata (7.8 kB) Collecting nnunetv2 (from -r requirements.txt (line 23)) Downloading nnunetv2-2.3.1.tar.gz (182 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 182.5/182.5 kB 2.5 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting numpy<1.24 (from -r requirements.txt (line 27)) Downloading numpy-1.23.5-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.3 kB) Collecting onnxruntime!=1.16.0,>=1.7.0 (from -r requirements.txt (line 31)) Downloading onnxruntime-1.17.1-cp39-cp39-macosx_11_0_universal2.whl.metadata (4.2 kB) Collecting pandas (from -r requirements.txt (line 32)) Downloading pandas-2.2.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (19 kB) Collecting portalocker (from -r requirements.txt (line 33)) Downloading portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB) Collecting psutil (from -r requirements.txt (line 34)) Downloading psutil-5.9.8-cp36-abi3-macosx_10_9_x86_64.whl.metadata (21 kB) Collecting pyqt5==5.12.3 (from -r requirements.txt (line 39)) Downloading PyQt5-5.12.3-5.12.10-cp35.cp36.cp37.cp38.cp39-abi3-macosx_10_6_intel.whl.metadata (2.2 kB) Collecting pyqt5-sip<12.13.0 (from -r requirements.txt (line 41)) Downloading PyQt5_sip-12.12.2-cp39-cp39-macosx_10_9_universal2.whl.metadata (504 bytes) Collecting pytest (from -r requirements.txt (line 42)) Downloading pytest-8.0.2-py3-none-any.whl.metadata (7.7 kB) Collecting pytest-cov (from -r requirements.txt (line 43)) Downloading pytest_cov-4.1.0-py3-none-any.whl.metadata (26 kB) Collecting requests (from -r requirements.txt (line 44)) Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting requirements-parser (from -r requirements.txt (line 45)) Downloading requirements_parser-0.5.0-py3-none-any.whl.metadata (3.1 kB) Collecting scipy (from -r requirements.txt (line 46)) Downloading scipy-1.12.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 8.0 MB/s eta 0:00:00 Collecting scikit-image (from -r requirements.txt (line 47)) Downloading scikit_image-0.22.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (13 kB) Collecting scikit-learn (from -r requirements.txt (line 48)) Downloading scikit_learn-1.4.1.post1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (11 kB) Collecting xlwt (from -r requirements.txt (line 49)) Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 1.2 MB/s eta 0:00:00 Collecting tqdm (from -r requirements.txt (line 50)) Downloading tqdm-4.66.2-py3-none-any.whl.metadata (57 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 5.3 MB/s eta 0:00:00 Collecting transforms3d (from -r requirements.txt (line 51)) Downloading transforms3d-0.4.1-py3-none-any.whl.metadata (2.8 kB) Collecting urllib3 (from -r requirements.txt (line 52)) Downloading urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB) Collecting pytest_console_scripts (from -r requirements.txt (line 53)) Downloading pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB) Collecting pyyaml (from -r requirements.txt (line 54)) Downloading PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.1 kB) Collecting voxelmorph (from -r requirements.txt (line 55)) Downloading voxelmorph-0.2-py3-none-any.whl.metadata (660 bytes) Collecting wquantiles (from -r requirements.txt (line 56)) Downloading wquantiles-0.6-py3-none-any.whl.metadata (1.1 kB) Collecting xlsxwriter (from -r requirements.txt (line 59)) Downloading XlsxWriter-3.2.0-py3-none-any.whl.metadata (2.6 kB) Collecting monai[nibabel] (from -r requirements.txt (line 13)) Downloading monai-1.3.0-202310121228-py3-none-any.whl.metadata (10 kB) Collecting h5py>=2.8.0 (from dipy!=1.6.*,!=1.7.*,!=1.8.*->-r requirements.txt (line 7)) Downloading h5py-3.10.0-cp39-cp39-macosx_10_9_x86_64.whl.metadata (2.5 kB) Collecting pyparsing<3,>=2.0.2 (from ivadomed->-r requirements.txt (line 11)) Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.8/67.8 kB 4.1 MB/s eta 0:00:00 Collecting csv-diff>=1.0 (from ivadomed->-r requirements.txt (line 11)) Downloading csv_diff-1.1-py3-none-any.whl.metadata (4.1 kB) Collecting loguru~=0.5 (from ivadomed->-r requirements.txt (line 11)) Downloading loguru-0.7.2-py3-none-any.whl.metadata (23 kB) Collecting imageio>=2.31.4 (from ivadomed->-r requirements.txt (line 11)) Downloading imageio-2.34.0-py3-none-any.whl.metadata (4.9 kB) Collecting joblib~=1.0 (from ivadomed->-r requirements.txt (line 11)) Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB) Collecting nibabel (from -r requirements.txt (line 21)) Downloading nibabel-3.2.2-py3-none-any.whl.metadata (6.2 kB) Collecting onnx (from ivadomed->-r requirements.txt (line 11)) Downloading onnx-1.15.0-cp39-cp39-macosx_10_12_x86_64.whl.metadata (15 kB) Collecting pandas (from -r requirements.txt (line 32)) Downloading pandas-1.4.4-cp39-cp39-macosx_10_9_x86_64.whl.metadata (12 kB) Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 11)) Downloading pybids-0.15.5-py3-none-any.whl.metadata (3.2 kB) Collecting seaborn~=0.11 (from ivadomed->-r requirements.txt (line 11)) Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 11)) Downloading tensorboard-2.16.2-py3-none-any.whl.metadata (1.6 kB) Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 11)) Downloading torchio-0.19.6-py2.py3-none-any.whl.metadata (48 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 2.7 MB/s eta 0:00:00 Collecting torch>=1.8.1 (from ivadomed->-r requirements.txt (line 11)) Downloading https://download.pytorch.org/whl/cpu/torch-2.2.1-cp39-none-macosx_10_9_x86_64.whl (151.0 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wheel for nnunetv2: filename=nnunetv2-2.3.1-py3-none-any.whl size=243618 sha256=423d7edefc999397cd7ba3274380ecf473bc0c8726f306343003ef83635e6534 Stored in directory: /private/tmp/pip-ephem-wheel-cache-u2xl3uz6/wheels/a1/30/0f/6c41432250a748dee161be18f2f982042c1d5126903fffd936 Building wheel for acvl-utils (setup.py): started Building wheel for acvl-utils (setup.py): finished with status 'done' Created wheel for acvl-utils: filename=acvl_utils-0.2-py3-none-any.whl size=22438 sha256=cacda1f64f0f8d00eb61ef37d156c584ec91191e3c4cdae2a6c825a07899717a Stored in directory: /private/tmp/pip-ephem-wheel-cache-u2xl3uz6/wheels/db/79/df/6ffb48299bba36fd2fc5d14dc8ae7d1caa3416aa7e96d605b7 Building wheel for batchgenerators (setup.py): started Building wheel for batchgenerators (setup.py): finished with status 'done' Created wheel for batchgenerators: filename=batchgenerators-0.25-py3-none-any.whl size=89008 sha256=ce3de0abbf4e02cebb46b56d52411fa85b023b6fd9b1dbba7a97d33f916b0cf9 Stored in directory: /private/tmp/pip-ephem-wheel-cache-u2xl3uz6/wheels/41/e7/c9/91b1589e2a08ad83bdd96b0beb3a496effda855580ef698568 Building wheel for dynamic-network-architectures (setup.py): started Building wheel for dynamic-network-architectures (setup.py): finished with status 'done' Created wheel for dynamic-network-architectures: filename=dynamic_network_architectures-0.3.1-py3-none-any.whl size=30048 sha256=bf97b7e911462d875003e52555b1f894f81fd91fc983aab6cc80356f17c82a7a Stored in directory: /private/tmp/pip-ephem-wheel-cache-u2xl3uz6/wheels/ec/59/c1/e65ad8b5ac7df95651f913251875b4cc8275644e0e28e82c63 Building wheel for pystrum (setup.py): started Building wheel for pystrum (setup.py): finished with status 'done' Created wheel for pystrum: filename=pystrum-0.4-py3-none-any.whl size=19533 sha256=ed1254ce343784b9e9509ef9372d63aed59bebdda4b09c5564566a67a3e1146d Stored in directory: /private/tmp/pip-ephem-wheel-cache-u2xl3uz6/wheels/4c/0b/97/737411e14729d327252b31723354f9be51fc46fb364f4c02ea Building wheel for docopt (setup.py): started Building wheel for docopt (setup.py): finished with status 'done' Created wheel for docopt: filename=docopt-0.6.2-py2.py3-none-any.whl size=13705 sha256=f50953afe95419f96da9fadad106c7bc6cb77228c8eda088bf73a9a4a73ed591 Stored in directory: /private/tmp/pip-ephem-wheel-cache-u2xl3uz6/wheels/70/4a/46/1309fc853b8d395e60bafaf1b6df7845bdd82c95fd59dd8d2b Successfully built nnunetv2 acvl-utils batchgenerators dynamic-network-architectures pystrum docopt Installing collected packages: xlwt, SimpleITK, pytz, mpmath, linecache2, flatbuffers, docopt, dictdiffer, bids-validator, 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, numpy, num2words, networkx, mdurl, MarkupSafe, lxml, loguru, lazy_loader, kiwisolver, joblib, interface-meta, iniconfig, idna, humanize, humanfriendly, grpcio, graphviz, future, fsspec, fonttools, filelock, exceptiongroup, cycler, coverage, colorama, click, charset-normalizer, certifi, astor, absl-py, yacs, wquantiles, werkzeug, unittest2, typer, tifffile, sentry-sdk, scipy, requirements-parser, requests, python-dateutil, pytest, pyqt5, onnx, nibabel, markdown-it-py, jinja2, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, gitdb, docker-pycreds, Deprecated, csv-diff, contourpy, connected-components-3d, coloredlogs, torch, scikit-learn, scikit-image, rich, pytest-cov, pytest_console_scripts, pandas, onnxruntime, matplotlib, markdown, GitPython, dipy, dicom2nifti, wandb, torchvision, tensorboard, seaborn, pystrum, nilearn, monai, formulaic, dynamic-network-architectures, batchgenerators, torchio, pybids, neurite, acvl-utils, voxelmorph, nnunetv2, ivadomed Successfully installed Deprecated-1.2.14 GitPython-3.1.42 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-1.14.1 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 coloredlogs-15.0.1 connected-components-3d-3.12.4 contourpy-1.2.0 coverage-7.4.3 csv-diff-1.1 cycler-0.12.1 dicom2nifti-2.4.10 dictdiffer-0.9.0 dipy-1.5.0 docker-pycreds-0.4.0 docopt-0.6.2 dynamic-network-architectures-0.3.1 exceptiongroup-1.2.0 filelock-3.13.1 flatbuffers-23.5.26 fonttools-4.49.0 formulaic-0.3.4 fsspec-2024.2.0 future-1.0.0 gitdb-4.0.11 graphviz-0.20.1 grpcio-1.62.0 h5py-3.10.0 humanfriendly-10.0 humanize-4.9.0 idna-3.6 imagecodecs-2024.1.1 imageio-2.34.0 importlib-metadata-7.0.1 importlib-resources-6.1.2 iniconfig-2.0.0 interface-meta-1.3.0 ivadomed-2.9.9 jinja2-3.1.3 joblib-1.3.2 kiwisolver-1.4.5 lazy_loader-0.3 linecache2-1.0.0 loguru-0.7.2 lxml-5.1.0 markdown-3.5.2 markdown-it-py-3.0.0 matplotlib-3.8.3 mdurl-0.1.2 monai-1.3.0 mpmath-1.3.0 networkx-3.2.1 neurite-0.2 nibabel-3.2.2 nilearn-0.10.2 nnunetv2-2.3.1 num2words-0.5.13 numpy-1.23.5 onnx-1.15.0 onnxruntime-1.17.1 packaging-23.2 pandas-1.4.4 pillow-10.2.0 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-2.4.7 pyqt5-5.12.3 pyqt5-sip-12.12.2 pystrum-0.4 pytest-8.0.2 pytest-cov-4.1.0 pytest_console_scripts-1.4.1 python-dateutil-2.8.2 python-gdcm-3.0.23 pytz-2024.1 pyyaml-6.0.1 requests-2.31.0 requirements-parser-0.5.0 rich-13.7.0 scikit-image-0.22.0 scikit-learn-1.4.1.post1 scipy-1.12.0 seaborn-0.13.2 sentry-sdk-1.40.6 setproctitle-1.3.3 setuptools-68.2.2 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-3.3.0 tifffile-2024.2.12 tomli-2.0.1 torch-2.2.1 torchio-0.19.6 torchvision-0.17.1 tqdm-4.66.2 traceback2-1.4.0 transforms3d-0.4.1 typer-0.9.0 types-setuptools-69.1.0.20240223 typing-extensions-4.10.0 unittest2-1.1.0 urllib3-2.2.1 voxelmorph-0.2 wandb-0.16.3 werkzeug-3.0.1 wquantiles-0.6 wrapt-1.16.0 xlsxwriter-3.2.0 xlwt-1.3.0 yacs-0.1.8 zipp-3.17.0 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv Installing spinalcordtoolbox... WARNING: The directory '/Users/mathilde/Library/Caches/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag. Obtaining file:///Users/mathilde/Downloads/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 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv 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 [00:23<00:00, 2.82MB/s] Creating temporary folder (/tmp/sct_2024-02-28_00-48-43_install-data_hblaykeq) Unzip data to: /tmp/sct_2024-02-28_00-48-43_install-data_hblaykeq Copying data to: /Users/mathilde/Downloads/spinalcordtoolbox/bin Removing temporary folders... Done! All requirements installed! Installing data... mkdir -p /Users/mathilde/Downloads/spinalcordtoolbox/data sct_download_data -d PAM50 -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_download_data -d PAM50 -- Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20240215/PAM50-r20240215.zip Downloading: PAM50-r20240215.zip Status: 100%|██████████| 104M/104M [00:36<00:00, 2.83MB/s] Creating temporary folder (/tmp/sct_2024-02-28_00-49-22_install-data_1cqn7ch5) Unzip data to: /tmp/sct_2024-02-28_00-49-22_install-data_1cqn7ch5 Copying data to: /Users/mathilde/Downloads/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 -- 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 [00:13<00:00, 1.44MB/s] Creating temporary folder (/tmp/sct_2024-02-28_00-49-37_install-data__aqal33q) Unzip data to: /tmp/sct_2024-02-28_00-49-37_install-data__aqal33q Copying data to: /Users/mathilde/Downloads/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 -- 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, 3.45MB/s] Creating temporary folder (/tmp/sct_2024-02-28_00-49-38_install-data_jz0vh2rl) Unzip data to: /tmp/sct_2024-02-28_00-49-38_install-data_jz0vh2rl Copying data to: /Users/mathilde/Downloads/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 -- 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 [00:02<00:00, 2.08MB/s] Creating temporary folder (/tmp/sct_2024-02-28_00-49-42_install-data_4bsww_1r) Unzip data to: /tmp/sct_2024-02-28_00-49-42_install-data_4bsww_1r Copying data to: /Users/mathilde/Downloads/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 -- Trying URL: https://github.com/ivadomed/multimodal-registration/releases/download/r20220512/models.zip Downloading: models.zip Status: 100%|██████████| 158M/158M [00:57<00:00, 2.74MB/s] Creating temporary folder (/tmp/sct_2024-02-28_00-50-41_install-data_z0o3rt4p) Unzip data to: /tmp/sct_2024-02-28_00-50-41_install-data_z0o3rt4p Copying data to: /Users/mathilde/Downloads/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 -- Trying URL: https://github.com/spinalcordtoolbox/PAM50-normalized-metrics/archive/refs/tags/r20230222.zip Downloading: PAM50-normalized-metrics-r20230222.zip Status: 6.92MB [00:02, 3.10MB/s] Creating temporary folder (/tmp/sct_2024-02-28_00-50-45_install-data_cn6mxvfc) Unzip data to: /tmp/sct_2024-02-28_00-50-45_install-data_cn6mxvfc Copying data to: /Users/mathilde/Downloads/spinalcordtoolbox/data/PAM50_normalized_metrics Removing temporary folders... Done! Status: 100%|██████████| 18.0M/18.0M [00:06<00:00, 2.87MB/s] Validate installation... -- Spinal Cord Toolbox (git-master-6962e03b5906ab3466e6e330438dbea58d949407) sct_check_dependencies -- SYSTEM INFORMATION ------------------ SCT info: - version: git-master-6962e03b5906ab3466e6e330438dbea58d949407 - path: /Users/mathilde/Downloads/spinalcordtoolbox OS: osx (macOS-10.16-x86_64-i386-64bit) CPU cores: Available: 8, Used by ITK functions: 8 RAM: Total: 8192MB, Used: 942MB, Available: 529MB OPTIONAL DEPENDENCIES --------------------- Check FSLeyes version...............................[ ] (127, '/bin/sh: fsleyes: command not found') MANDATORY DEPENDENCIES ---------------------- Check Python executable.............................[OK] Using bundled python 3.9.18 (main, Sep 11 2023, 08:38:23) [Clang 14.0.6 ] at /Users/mathilde/Downloads/spinalcordtoolbox/python/envs/venv_sct/bin/python Check if data are installed.........................[OK] Check if dipy is installed..........................[OK] (1.5.0) Check if ivadomed is installed......................[OK] (2.9.9) Check if matplotlib is installed....................[OK] (3.8.3) Check if monai is installed.........................[OK] (1.3.0) Check if nibabel is installed.......................[OK] (3.2.2) Check if nilearn is installed.......................[OK] (0.10.2) Check if nnunetv2 is installed......................[OK] Check if numpy is installed.........................[OK] (1.23.5) Check if onnxruntime is installed...................[OK] (1.17.1) Check if pandas is installed........................[OK] (1.4.4) 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] (8.0.2) Check if pytest-cov is installed....................[OK] (4.1.0) Check if requests is installed......................[OK] (2.31.0) Check if requirements-parser is installed...........[OK] Check if scipy is installed.........................[OK] (1.12.0) Check if scikit-image is installed..................[OK] (0.22.0) Check if scikit-learn is installed..................[OK] (1.4.1.post1) 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$