******************************* * Welcome to SCT installation * *******************************  Checking OS type and version... Darwin MSs-MacBook-Pro.local 20.6.0 Darwin Kernel Version 20.6.0: Wed Jun 23 00:26:27 PDT 2021; root:xnu-7195.141.2~5/RELEASE_ARM64_T8101 arm64 ProductVersion: 11.5.2 Checking requirements... OK! SCT version ......... 7.3.dev0 Installation type ... in-place Operating system .... osx (11.5.2) Shell config ........ /Users/msresearch/.zshrc Checking permissions on required file /Users/msresearch/.zshrc:  - File exists: True - File ownership: True - Read permissions: True - Write permissions: True WARNING: Directory already exists. Files will be overwritten. SCT will be installed here: [/Users/msresearch/Downloads/spinalcordtoolbox]  Do you agree? [y]es/[n]o:  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:  Downloading Miniforge... curl -sS -o /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/tmp.MpIixQvj/miniforge.sh -L https://github.com/conda-forge/miniforge/releases/download/24.11.2-1/Miniforge3-MacOSX-x86_64.sh Installing Miniforge... bash /var/folders/mm/vhlf215s7k338w7srsxw2chm0000gn/T/tmp.MpIixQvj/miniforge.sh -p /Users/msresearch/Downloads/spinalcordtoolbox/python -b -f PREFIX=/Users/msresearch/Downloads/spinalcordtoolbox/python Unpacking payload ... Extracting bzip2-1.0.8-hfdf4475_7.conda Extracting c-ares-1.34.4-hf13058a_0.conda Extracting ca-certificates-2024.12.14-h8857fd0_0.conda Extracting libcxx-19.1.6-hf95d169_1.conda Extracting libev-4.33-h10d778d_2.conda Extracting libexpat-2.6.4-h240833e_0.conda Extracting libffi-3.4.2-h0d85af4_5.tar.bz2 Extracting libiconv-1.17-hd75f5a5_2.conda Extracting liblzma-5.6.3-hd471939_1.conda Extracting libzlib-1.3.1-hd23fc13_2.conda Extracting lzo-2.10-h10d778d_1001.conda Extracting ncurses-6.5-hf036a51_1.conda Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2 Extracting python_abi-3.12-5_cp312.conda Extracting reproc-14.2.5.post0-h6e16a3a_0.conda Extracting tzdata-2024b-hc8b5060_0.conda Extracting fmt-11.0.2-h3c5361c_0.conda Extracting libedit-3.1.20191231-h0678c8f_2.tar.bz2 Extracting libsolv-0.7.30-h69d5d9b_0.conda Extracting libsqlite-3.47.2-hdb6dae5_0.conda Extracting libxml2-2.13.5-he8ee3e7_1.conda Extracting lz4-c-1.10.0-h240833e_1.conda Extracting openssl-3.4.0-hd471939_0.conda Extracting readline-8.2-h9e318b2_1.conda Extracting reproc-cpp-14.2.5.post0-h240833e_0.conda Extracting tk-8.6.13-h1abcd95_1.conda Extracting yaml-cpp-0.8.0-he965462_0.conda Extracting zstd-1.5.6-h915ae27_0.conda Extracting krb5-1.21.3-h37d8d59_0.conda Extracting libarchive-3.7.7-h1a33361_3.conda Extracting libnghttp2-1.64.0-hc7306c3_0.conda Extracting libssh2-1.11.1-h3dc7d44_0.conda Extracting python-3.12.8-h9ccd52b_1_cpython.conda Extracting libcurl-8.11.1-h5dec5d8_0.conda Extracting menuinst-2.2.0-py312hb401068_0.conda Extracting archspec-0.2.3-pyhd8ed1ab_0.conda Extracting boltons-24.0.0-pyhd8ed1ab_1.conda Extracting brotli-python-1.1.0-py312h5861a67_2.conda Extracting certifi-2024.12.14-pyhd8ed1ab_0.conda Extracting charset-normalizer-3.4.1-pyhd8ed1ab_0.conda Extracting colorama-0.4.6-pyhd8ed1ab_1.conda Extracting distro-1.9.0-pyhd8ed1ab_1.conda Extracting frozendict-2.4.6-py312h3d0f464_0.conda Extracting hpack-4.0.0-pyhd8ed1ab_1.conda Extracting hyperframe-6.0.1-pyhd8ed1ab_1.conda Extracting idna-3.10-pyhd8ed1ab_1.conda Extracting jsonpointer-3.0.0-py312hb401068_1.conda Extracting libmamba-1.5.12-h415aaf8_0.conda Extracting packaging-24.2-pyhd8ed1ab_2.conda Extracting platformdirs-4.3.6-pyhd8ed1ab_1.conda Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda Extracting pycosat-0.6.6-py312h01d7ebd_2.conda Extracting pycparser-2.22-pyh29332c3_1.conda Extracting pysocks-1.7.1-pyha55dd90_7.conda Extracting ruamel.yaml.clib-0.2.8-py312h3d0f464_1.conda Extracting setuptools-75.6.0-pyhff2d567_1.conda Extracting truststore-0.10.0-pyhd8ed1ab_0.conda Extracting wheel-0.45.1-pyhd8ed1ab_1.conda Extracting cffi-1.17.1-py312hf857d28_0.conda Extracting h2-4.1.0-pyhd8ed1ab_1.conda Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda Extracting libmambapy-1.5.12-py312h4e4b3da_0.conda Extracting pip-24.3.1-pyh8b19718_2.conda Extracting ruamel.yaml-0.18.8-py312h01d7ebd_0.conda Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda Extracting zstandard-0.23.0-py312h7122b0e_1.conda Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda Extracting conda-package-handling-2.4.0-pyha770c72_1.conda Extracting requests-2.32.3-pyhd8ed1ab_1.conda Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda Extracting conda-24.11.2-py312hb401068_1.conda Extracting mamba-1.5.12-py312ha12221d_0.conda Installing base environment... Transaction Prefix: /Users/msresearch/Downloads/spinalcordtoolbox/python Updating specs: - conda-forge/osx-64::bzip2==1.0.8=hfdf4475_7[md5=7ed4301d437b59045be7e051a0308211] - conda-forge/osx-64::c-ares==1.34.4=hf13058a_0[md5=133255af67aaf1e0c0468cc753fd800b] - conda-forge/osx-64::ca-certificates==2024.12.14=h8857fd0_0[md5=b7b887091c99ed2e74845e75e9128410] - conda-forge/osx-64::libcxx==19.1.6=hf95d169_1[md5=1bad6c181a0799298aad42fc5a7e98b7] - conda-forge/osx-64::libev==4.33=h10d778d_2[md5=899db79329439820b7e8f8de41bca902] - conda-forge/osx-64::libexpat==2.6.4=h240833e_0[md5=20307f4049a735a78a29073be1be2626] - conda-forge/osx-64::libffi==3.4.2=h0d85af4_5[md5=ccb34fb14960ad8b125962d3d79b31a9] - conda-forge/osx-64::libiconv==1.17=hd75f5a5_2[md5=6c3628d047e151efba7cf08c5e54d1ca] - conda-forge/osx-64::liblzma==5.6.3=hd471939_1[md5=f9e9205fed9c664421c1c09f0b90ce6d] - conda-forge/osx-64::libzlib==1.3.1=hd23fc13_2[md5=003a54a4e32b02f7355b50a837e699da] - conda-forge/osx-64::lzo==2.10=h10d778d_1001[md5=bfecd73e4a2dc18ffd5288acf8a212ab] - conda-forge/osx-64::ncurses==6.5=hf036a51_1[md5=e102bbf8a6ceeaf429deab8032fc8977] - conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be] - conda-forge/osx-64::python_abi==3.12=5_cp312[md5=c34dd4920e0addf7cfcc725809f25d8e] - conda-forge/osx-64::reproc==14.2.5.post0=h6e16a3a_0[md5=eda18d4a7dce3831016086a482965345] - conda-forge/noarch::tzdata==2024b=hc8b5060_0[md5=8ac3367aafb1cc0a068483c580af8015] - conda-forge/osx-64::fmt==11.0.2=h3c5361c_0[md5=e8070546e8739040383f6774e0cd4033] - conda-forge/osx-64::libedit==3.1.20191231=h0678c8f_2[md5=6016a8a1d0e63cac3de2c352cd40208b] - conda-forge/osx-64::libsolv==0.7.30=h69d5d9b_0[md5=8f8fd9f1740c8cb7dcfebf1a1ed7e678] - conda-forge/osx-64::libsqlite==3.47.2=hdb6dae5_0[md5=44d9799fda97eb34f6d88ac1e3eb0ea6] - conda-forge/osx-64::libxml2==2.13.5=he8ee3e7_1[md5=9379f216f9132d0d3cdeeb10af165262] - conda-forge/osx-64::lz4-c==1.10.0=h240833e_1[md5=d6b9bd7e356abd7e3a633d59b753495a] - conda-forge/osx-64::openssl==3.4.0=hd471939_0[md5=ec99d2ce0b3033a75cbad01bbc7c5b71] - conda-forge/osx-64::readline==8.2=h9e318b2_1[md5=f17f77f2acf4d344734bda76829ce14e] - conda-forge/osx-64::reproc-cpp==14.2.5.post0=h240833e_0[md5=420229341978751bd96faeced92c200e] - conda-forge/osx-64::tk==8.6.13=h1abcd95_1[md5=bf830ba5afc507c6232d4ef0fb1a882d] - conda-forge/osx-64::yaml-cpp==0.8.0=he965462_0[md5=1bb3addc859ed1338370da6e2996ef47] - conda-forge/osx-64::zstd==1.5.6=h915ae27_0[md5=4cb2cd56f039b129bb0e491c1164167e] - conda-forge/osx-64::krb5==1.21.3=h37d8d59_0[md5=d4765c524b1d91567886bde656fb514b] - conda-forge/osx-64::libarchive==3.7.7=h1a33361_3[md5=5cc55f063de099a537a56c4db2e8d58d] - conda-forge/osx-64::libnghttp2==1.64.0=hc7306c3_0[md5=ab21007194b97beade22ceb7a3f6fee5] - conda-forge/osx-64::libssh2==1.11.1=h3dc7d44_0[md5=b1caec4561059e43a5d056684c5a2de0] - conda-forge/osx-64::python==3.12.8=h9ccd52b_1_cpython[md5=68a31f9cfbdcab2a4baec79095374780] - conda-forge/osx-64::libcurl==8.11.1=h5dec5d8_0[md5=2f80e92674f4a92e9f8401494496ee62] - conda-forge/osx-64::menuinst==2.2.0=py312hb401068_0[md5=4b908217561a1274f48b0f9952fb5359] - conda-forge/noarch::archspec==0.2.3=pyhd8ed1ab_0[md5=192278292e20704f663b9c766909d67b] - conda-forge/noarch::boltons==24.0.0=pyhd8ed1ab_1[md5=d88c38e66d85ecc9c7e2c4110676bbf4] - conda-forge/osx-64::brotli-python==1.1.0=py312h5861a67_2[md5=b95025822e43128835826ec0cc45a551] - conda-forge/noarch::certifi==2024.12.14=pyhd8ed1ab_0[md5=6feb87357ecd66733be3279f16a8c400] - conda-forge/noarch::charset-normalizer==3.4.1=pyhd8ed1ab_0[md5=e83a31202d1c0a000fce3e9cf3825875] - conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_1[md5=962b9857ee8e7018c22f2776ffa0b2d7] - conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_1[md5=0a2014fd9860f8b1eaa0b1f3d3771a08] - conda-forge/osx-64::frozendict==2.4.6=py312h3d0f464_0[md5=58a8d9e016adc22964bfb0b9a5272e16] - conda-forge/noarch::hpack==4.0.0=pyhd8ed1ab_1[md5=2aa5ff7fa34a81b9196532c84c10d865] - conda-forge/noarch::hyperframe==6.0.1=pyhd8ed1ab_1[md5=566e75c90c1d0c8c459eb0ad9833dc7a] - conda-forge/noarch::idna==3.10=pyhd8ed1ab_1[md5=39a4f67be3286c86d696df570b1201b7] - conda-forge/osx-64::jsonpointer==3.0.0=py312hb401068_1[md5=5dcf96bca4649d496d818a0f5cfb962e] - conda-forge/osx-64::libmamba==1.5.12=h415aaf8_0[md5=4d0ba50ef9b7a0702b5e7d13b139de24] - conda-forge/noarch::packaging==24.2=pyhd8ed1ab_2[md5=3bfed7e6228ebf2f7b9eaa47f1b4e2aa] - conda-forge/noarch::platformdirs==4.3.6=pyhd8ed1ab_1[md5=577852c7e53901ddccc7e6a9959ddebe] - conda-forge/noarch::pluggy==1.5.0=pyhd8ed1ab_1[md5=e9dcbce5f45f9ee500e728ae58b605b6] - conda-forge/osx-64::pycosat==0.6.6=py312h01d7ebd_2[md5=9addc104aa4afd0b21a086cfdca253d5] - conda-forge/noarch::pycparser==2.22=pyh29332c3_1[md5=12c566707c80111f9799308d9e265aef] - conda-forge/noarch::pysocks==1.7.1=pyha55dd90_7[md5=461219d1a5bd61342293efa2c0c90eac] - conda-forge/osx-64::ruamel.yaml.clib==0.2.8=py312h3d0f464_1[md5=f4c0464f98dabcd65064e89991c3c9c2] - conda-forge/noarch::setuptools==75.6.0=pyhff2d567_1[md5=fc80f7995e396cbaeabd23cf46c413dc] - conda-forge/noarch::truststore==0.10.0=pyhd8ed1ab_0[md5=ad1c20cd193e3044bcf17798c33b9d67] - conda-forge/noarch::wheel==0.45.1=pyhd8ed1ab_1[md5=75cb7132eb58d97896e173ef12ac9986] - conda-forge/osx-64::cffi==1.17.1=py312hf857d28_0[md5=5bbc69b8194fedc2792e451026cac34f] - conda-forge/noarch::h2==4.1.0=pyhd8ed1ab_1[md5=825927dc7b0f287ef8d4d0011bb113b1] - conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_1[md5=cb60ae9cf02b9fcb8004dec4089e5691] - conda-forge/osx-64::libmambapy==1.5.12=py312h4e4b3da_0[md5=015a81b7c86e74144fc106be5810aa30] - conda-forge/noarch::pip==24.3.1=pyh8b19718_2[md5=04e691b9fadd93a8a9fad87a81d4fd8f] - conda-forge/osx-64::ruamel.yaml==0.18.8=py312h01d7ebd_0[md5=8147454ea92f105fbab3bd1044892bc8] - conda-forge/noarch::tqdm==4.67.1=pyhd8ed1ab_1[md5=9efbfdc37242619130ea42b1cc4ed861] - conda-forge/osx-64::zstandard==0.23.0=py312h7122b0e_1[md5=bd132ba98f3fc0a6067f355f8efe4cb6] - conda-forge/noarch::conda-package-streaming==0.11.0=pyhd8ed1ab_0[md5=bc9533d8616a97551ed144789bf9c1cd] - conda-forge/noarch::urllib3==2.3.0=pyhd8ed1ab_0[md5=32674f8dbfb7b26410ed580dd3c10a29] - conda-forge/noarch::conda-package-handling==2.4.0=pyha770c72_1[md5=28b86d110bda4ef40e680d1afa9ddb1d] - conda-forge/noarch::requests==2.32.3=pyhd8ed1ab_1[md5=a9b9368f3701a417eac9edbcae7cb737] - conda-forge/noarch::conda-libmamba-solver==24.9.0=pyhd8ed1ab_0[md5=45378d089c5f72c9c0d63d58414c645d] - conda-forge/osx-64::conda==24.11.2=py312hb401068_1[md5=5dffa6caac1bf5bb3141514e659bf393] - conda-forge/osx-64::mamba==1.5.12=py312ha12221d_0[md5=1020c747a424cbc156284f0620d4234f] Package Version Build Channel Size ───────────────────────────────────────────────────────────────────────────────────── Install: ───────────────────────────────────────────────────────────────────────────────────── + bzip2 1.0.8 hfdf4475_7 conda-forge + c-ares 1.34.4 hf13058a_0 conda-forge + ca-certificates 2024.12.14 h8857fd0_0 conda-forge + libcxx 19.1.6 hf95d169_1 conda-forge + libev 4.33 h10d778d_2 conda-forge + libexpat 2.6.4 h240833e_0 conda-forge + libffi 3.4.2 h0d85af4_5 conda-forge + libiconv 1.17 hd75f5a5_2 conda-forge + liblzma 5.6.3 hd471939_1 conda-forge + libzlib 1.3.1 hd23fc13_2 conda-forge + lzo 2.10 h10d778d_1001 conda-forge + ncurses 6.5 hf036a51_1 conda-forge + pybind11-abi 4 hd8ed1ab_3 conda-forge + python_abi 3.12 5_cp312 conda-forge + reproc 14.2.5.post0 h6e16a3a_0 conda-forge + tzdata 2024b hc8b5060_0 conda-forge + fmt 11.0.2 h3c5361c_0 conda-forge + libedit 3.1.20191231 h0678c8f_2 conda-forge + libsolv 0.7.30 h69d5d9b_0 conda-forge + libsqlite 3.47.2 hdb6dae5_0 conda-forge + libxml2 2.13.5 he8ee3e7_1 conda-forge + lz4-c 1.10.0 h240833e_1 conda-forge + openssl 3.4.0 hd471939_0 conda-forge + readline 8.2 h9e318b2_1 conda-forge + reproc-cpp 14.2.5.post0 h240833e_0 conda-forge + tk 8.6.13 h1abcd95_1 conda-forge + yaml-cpp 0.8.0 he965462_0 conda-forge + zstd 1.5.6 h915ae27_0 conda-forge + krb5 1.21.3 h37d8d59_0 conda-forge + libarchive 3.7.7 h1a33361_3 conda-forge + libnghttp2 1.64.0 hc7306c3_0 conda-forge + libssh2 1.11.1 h3dc7d44_0 conda-forge + python 3.12.8 h9ccd52b_1_cpython conda-forge + libcurl 8.11.1 h5dec5d8_0 conda-forge + menuinst 2.2.0 py312hb401068_0 conda-forge + archspec 0.2.3 pyhd8ed1ab_0 conda-forge + boltons 24.0.0 pyhd8ed1ab_1 conda-forge + brotli-python 1.1.0 py312h5861a67_2 conda-forge + certifi 2024.12.14 pyhd8ed1ab_0 conda-forge + charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge + colorama 0.4.6 pyhd8ed1ab_1 conda-forge + distro 1.9.0 pyhd8ed1ab_1 conda-forge + frozendict 2.4.6 py312h3d0f464_0 conda-forge + hpack 4.0.0 pyhd8ed1ab_1 conda-forge + hyperframe 6.0.1 pyhd8ed1ab_1 conda-forge + idna 3.10 pyhd8ed1ab_1 conda-forge + jsonpointer 3.0.0 py312hb401068_1 conda-forge + libmamba 1.5.12 h415aaf8_0 conda-forge + packaging 24.2 pyhd8ed1ab_2 conda-forge + platformdirs 4.3.6 pyhd8ed1ab_1 conda-forge + pluggy 1.5.0 pyhd8ed1ab_1 conda-forge + pycosat 0.6.6 py312h01d7ebd_2 conda-forge + pycparser 2.22 pyh29332c3_1 conda-forge + pysocks 1.7.1 pyha55dd90_7 conda-forge + ruamel.yaml.clib 0.2.8 py312h3d0f464_1 conda-forge + setuptools 75.6.0 pyhff2d567_1 conda-forge + truststore 0.10.0 pyhd8ed1ab_0 conda-forge + wheel 0.45.1 pyhd8ed1ab_1 conda-forge + cffi 1.17.1 py312hf857d28_0 conda-forge + h2 4.1.0 pyhd8ed1ab_1 conda-forge + jsonpatch 1.33 pyhd8ed1ab_1 conda-forge + libmambapy 1.5.12 py312h4e4b3da_0 conda-forge + pip 24.3.1 pyh8b19718_2 conda-forge + ruamel.yaml 0.18.8 py312h01d7ebd_0 conda-forge + tqdm 4.67.1 pyhd8ed1ab_1 conda-forge + zstandard 0.23.0 py312h7122b0e_1 conda-forge + conda-package-streaming 0.11.0 pyhd8ed1ab_0 conda-forge + urllib3 2.3.0 pyhd8ed1ab_0 conda-forge + conda-package-handling 2.4.0 pyha770c72_1 conda-forge + requests 2.32.3 pyhd8ed1ab_1 conda-forge + conda-libmamba-solver 24.9.0 pyhd8ed1ab_0 conda-forge + conda 24.11.2 py312hb401068_1 conda-forge + mamba 1.5.12 py312ha12221d_0 conda-forge Summary: Install: 73 packages Total download: 0 B ───────────────────────────────────────────────────────────────────────────────────── Transaction starting Transaction finished To activate this environment, use: micromamba activate /Users/msresearch/Downloads/spinalcordtoolbox/python Or to execute a single command in this environment, use: micromamba run -p /Users/msresearch/Downloads/spinalcordtoolbox/python mycommand installation finished. Creating conda environment... Channels: - conda-forge Platform: osx-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.11.2 latest version: 25.11.0 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /Users/msresearch/Downloads/spinalcordtoolbox/python/envs/venv_sct added / updated specs: - python=3.10 The following packages will be downloaded: package | build ---------------------------|----------------- bzip2-1.0.8 | h500dc9f_8 129 KB conda-forge ca-certificates-2025.11.12 | hbd8a1cb_0 149 KB conda-forge icu-75.1 | h120a0e1_0 11.2 MB conda-forge libexpat-2.7.3 | heffb93a_0 72 KB conda-forge libffi-3.5.2 | h750e83c_0 51 KB conda-forge liblzma-5.8.1 | hd471939_2 102 KB conda-forge libsqlite-3.51.1 | h6cc646a_0 968 KB conda-forge ncurses-6.5 | h0622a9a_3 803 KB conda-forge openssl-3.6.0 | h230baf5_0 2.7 MB conda-forge pip-25.3 | pyh8b19718_0 1.1 MB conda-forge python-3.10.19 |h988dfef_2_cpython 12.5 MB conda-forge readline-8.2 | h7cca4af_2 251 KB conda-forge setuptools-80.9.0 | pyhff2d567_0 731 KB conda-forge tk-8.6.13 | hf689a15_3 3.1 MB conda-forge tzdata-2025b | h78e105d_0 120 KB conda-forge ------------------------------------------------------------ Total: 33.9 MB The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h500dc9f_8 ca-certificates conda-forge/noarch::ca-certificates-2025.11.12-hbd8a1cb_0 icu conda-forge/osx-64::icu-75.1-h120a0e1_0 libexpat conda-forge/osx-64::libexpat-2.7.3-heffb93a_0 libffi conda-forge/osx-64::libffi-3.5.2-h750e83c_0 liblzma conda-forge/osx-64::liblzma-5.8.1-hd471939_2 libsqlite conda-forge/osx-64::libsqlite-3.51.1-h6cc646a_0 libzlib conda-forge/osx-64::libzlib-1.3.1-hd23fc13_2 ncurses conda-forge/osx-64::ncurses-6.5-h0622a9a_3 openssl conda-forge/osx-64::openssl-3.6.0-h230baf5_0 pip conda-forge/noarch::pip-25.3-pyh8b19718_0 python conda-forge/osx-64::python-3.10.19-h988dfef_2_cpython readline conda-forge/osx-64::readline-8.2-h7cca4af_2 setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0 tk conda-forge/osx-64::tk-8.6.13-hf689a15_3 tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 Downloading and Extracting Packages: ...working... python-3.10.19 | 12.5 MB | | 0% icu-75.1 | 11.2 MB | | 0%  tk-8.6.13 | 3.1 MB | | 0%  openssl-3.6.0 | 2.7 MB | | 0%  pip-25.3 | 1.1 MB | | 0%  libsqlite-3.51.1 | 968 KB | | 0%  ncurses-6.5 | 803 KB | | 0%  setuptools-80.9.0 | 731 KB | | 0%  readline-8.2 | 251 KB | | 0%  ca-certificates-2025 | 149 KB | | 0%  bzip2-1.0.8 | 129 KB | | 0%  tzdata-2025b | 120 KB | | 0%  liblzma-5.8.1 | 102 KB | | 0%  libexpat-2.7.3 | 72 KB | | 0%  libffi-3.5.2 | 51 KB | | 0%  openssl-3.6.0 | 2.7 MB | 4 | 4%  icu-75.1 | 11.2 MB | | 0%  pip-25.3 | 1.1 MB | 1 | 1%  tk-8.6.13 | 3.1 MB | | 1%  python-3.10.19 | 12.5 MB | | 0% openssl-3.6.0 | 2.7 MB | ######9 | 70%  icu-75.1 | 11.2 MB | 4 | 5%  pip-25.3 | 1.1 MB | ###3 | 33%  tk-8.6.13 | 3.1 MB | #5 | 15%  python-3.10.19 | 12.5 MB | 2 | 3% openssl-3.6.0 | 2.7 MB | ########## | 100%  icu-75.1 | 11.2 MB | #7 | 18%  pip-25.3 | 1.1 MB | ######8 | 68%  tk-8.6.13 | 3.1 MB | ###2 | 32%  python-3.10.19 | 12.5 MB | 7 | 8% openssl-3.6.0 | 2.7 MB | ########## | 100%  libsqlite-3.51.1 | 968 KB | 1 | 2%  icu-75.1 | 11.2 MB | ###6 | 37%  tk-8.6.13 | 3.1 MB | ####5 | 45%  pip-25.3 | 1.1 MB | #########6 | 96%  python-3.10.19 | 12.5 MB | #1 | 11% pip-25.3 | 1.1 MB | ########## | 100%  libsqlite-3.51.1 | 968 KB | ########## | 100%  libsqlite-3.51.1 | 968 KB | ########## | 100%  libsqlite-3.51.1 | 968 KB | ########## | 100%  ncurses-6.5 | 803 KB | 1 | 2%  icu-75.1 | 11.2 MB | #####6 | 57%  setuptools-80.9.0 | 731 KB | 2 | 2%  python-3.10.19 | 12.5 MB | #5 | 16% tk-8.6.13 | 3.1 MB | #####8 | 59%  setuptools-80.9.0 | 731 KB | ########## | 100%  pip-25.3 | 1.1 MB | ########## | 100%  icu-75.1 | 11.2 MB | #######2 | 73%  ncurses-6.5 | 803 KB | ###9 | 40%  python-3.10.19 | 12.5 MB | ##2 | 22% tk-8.6.13 | 3.1 MB | #######8 | 79%  readline-8.2 | 251 KB | 6 | 6%  readline-8.2 | 251 KB | ########## | 100%  icu-75.1 | 11.2 MB | #########1 | 92%  ncurses-6.5 | 803 KB | ########3 | 84%  readline-8.2 | 251 KB | ########## | 100%  ncurses-6.5 | 803 KB | ########## | 100%  python-3.10.19 | 12.5 MB | ##7 | 28% ca-certificates-2025 | 149 KB | # | 11%  setuptools-80.9.0 | 731 KB | ########## | 100%  setuptools-80.9.0 | 731 KB | ########## | 100%  ca-certificates-2025 | 149 KB | ########## | 100%  tk-8.6.13 | 3.1 MB | #########7 | 97%  ca-certificates-2025 | 149 KB | ########## | 100%  tk-8.6.13 | 3.1 MB | ########## | 100%  bzip2-1.0.8 | 129 KB | #2 | 12%  tzdata-2025b | 120 KB | #3 | 13%  icu-75.1 | 11.2 MB | ########## | 100%  tzdata-2025b | 120 KB | ########## | 100%  bzip2-1.0.8 | 129 KB | ########## | 100%  liblzma-5.8.1 | 102 KB | #5 | 16%  python-3.10.19 | 12.5 MB | ###6 | 36% liblzma-5.8.1 | 102 KB | ########## | 100%  libexpat-2.7.3 | 72 KB | ##2 | 22%  libexpat-2.7.3 | 72 KB | ########## | 100%  libffi-3.5.2 | 51 KB | ###1 | 31%  libffi-3.5.2 | 51 KB | ########## | 100%  python-3.10.19 | 12.5 MB | ####7 | 47% python-3.10.19 | 12.5 MB | ######3 | 64% tk-8.6.13 | 3.1 MB | ########## | 100%  python-3.10.19 | 12.5 MB | ########5 | 86% icu-75.1 | 11.2 MB | ########## | 100%  bzip2-1.0.8 | 129 KB | ########## | 100%  bzip2-1.0.8 | 129 KB | ########## | 100%  liblzma-5.8.1 | 102 KB | ########## | 100%  liblzma-5.8.1 | 102 KB | ########## | 100%  libexpat-2.7.3 | 72 KB | ########## | 100%  libexpat-2.7.3 | 72 KB | ########## | 100%  libffi-3.5.2 | 51 KB | ########## | 100%  libffi-3.5.2 | 51 KB | ########## | 100%  python-3.10.19 | 12.5 MB | ########## | 100% python-3.10.19 | 12.5 MB | ########## | 100% tzdata-2025b | 120 KB | ########## | 100%  tzdata-2025b | 120 KB | ########## | 100%  ncurses-6.5 | 803 KB | ########## | 100%  python-3.10.19 | 12.5 MB | ########## | 100%               done Preparing transaction: - \ done Verifying transaction: / - \ | / - \ | / done Executing transaction: \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done # # To activate this environment, use # # $ conda activate /Users/msresearch/Downloads/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/python3.10/site-packages (25.3) 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-2025.11.12-py3-none-any.whl.metadata (2.5 kB) Collecting acvl_utils!=0.2.1 (from -r requirements.txt (line 7)) Using cached acvl_utils-0.2.5.tar.gz (29 kB) 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' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting blosc2!=3.9.0 (from -r requirements.txt (line 12)) Using cached blosc2-3.12.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (7.1 kB) Collecting dipy==1.8.0 (from -r requirements.txt (line 14)) Using cached dipy-1.8.0-cp310-cp310-macosx_10_9_x86_64.whl.metadata (8.6 kB) Collecting h5py!=3.15.0 (from -r requirements.txt (line 16)) Using cached h5py-3.15.1-cp310-cp310-macosx_10_9_x86_64.whl.metadata (3.0 kB) Collecting ivadomed (from -r requirements.txt (line 20)) Using cached ivadomed-2.9.10-py3-none-any.whl.metadata (6.4 kB) Collecting matplotlib (from -r requirements.txt (line 21)) Using cached matplotlib-3.10.7-cp310-cp310-macosx_10_12_x86_64.whl.metadata (11 kB) Collecting matplotlib-inline (from -r requirements.txt (line 26)) Using cached matplotlib_inline-0.2.1-py3-none-any.whl.metadata (2.3 kB) Collecting nibabel (from -r requirements.txt (line 34)) Using cached nibabel-5.3.3-py3-none-any.whl.metadata (9.1 kB) Collecting nilearn (from -r requirements.txt (line 35)) Downloading nilearn-0.12.1-py3-none-any.whl.metadata (9.9 kB) Collecting nnunetv2-neuropoly (from -r requirements.txt (line 44)) Using cached nnunetv2_neuropoly-2.6.2-py3-none-any.whl.metadata (25 kB) Collecting numpy<2 (from -r requirements.txt (line 46)) Using cached numpy-1.26.4-cp310-cp310-macosx_10_9_x86_64.whl.metadata (61 kB) Collecting numexpr!=2.14.0 (from -r requirements.txt (line 49)) Using cached numexpr-2.14.1-cp310-cp310-macosx_10_9_x86_64.whl.metadata (9.0 kB) Collecting onnxruntime!=1.16.0,<1.22.0,>=1.7.0 (from -r requirements.txt (line 55)) Downloading onnxruntime-1.19.2-cp310-cp310-macosx_11_0_universal2.whl.metadata (4.5 kB) Collecting onnx<1.16.2 (from -r requirements.txt (line 58)) Using cached onnx-1.16.1-cp310-cp310-macosx_11_0_universal2.whl.metadata (16 kB) Collecting pandas (from -r requirements.txt (line 59)) Downloading pandas-2.3.3-cp310-cp310-macosx_10_9_x86_64.whl.metadata (91 kB) Collecting portalocker (from -r requirements.txt (line 60)) Downloading portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB) Collecting psutil (from -r requirements.txt (line 61)) Downloading psutil-7.1.3-cp36-abi3-macosx_10_9_x86_64.whl.metadata (23 kB) Collecting pyqt5>=5.15.0 (from -r requirements.txt (line 64)) Downloading PyQt5-5.15.11-cp38-abi3-macosx_11_0_x86_64.whl.metadata (2.1 kB) Collecting PyQt5-Qt5==5.15.2 (from -r requirements.txt (line 69)) Downloading PyQt5_Qt5-5.15.2-py3-none-macosx_10_13_intel.whl.metadata (535 bytes) Collecting pystrum>=0.3 (from -r requirements.txt (line 72)) Using cached pystrum-0.4.tar.gz (17 kB) 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' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting pytest (from -r requirements.txt (line 73)) Downloading pytest-9.0.2-py3-none-any.whl.metadata (7.6 kB) Collecting pytest-cov (from -r requirements.txt (line 74)) Downloading pytest_cov-7.0.0-py3-none-any.whl.metadata (31 kB) Collecting requests (from -r requirements.txt (line 75)) Downloading requests-2.32.5-py3-none-any.whl.metadata (4.9 kB) Collecting requirements-parser (from -r requirements.txt (line 76)) Downloading requirements_parser-0.13.0-py3-none-any.whl.metadata (4.7 kB) Collecting scipy (from -r requirements.txt (line 77)) Downloading scipy-1.15.3-cp310-cp310-macosx_10_13_x86_64.whl.metadata (61 kB) Collecting scikit-image (from -r requirements.txt (line 78)) Downloading scikit_image-0.25.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (14 kB) Collecting scikit-learn (from -r requirements.txt (line 79)) Downloading scikit_learn-1.7.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (11 kB) Collecting xlwt (from -r requirements.txt (line 81)) Using cached xlwt-1.3.0-py2.py3-none-any.whl.metadata (3.5 kB) Collecting torch<2.3 (from -r requirements.txt (line 93)) Downloading https://download.pytorch.org/whl/cpu/torch-2.2.2-cp310-none-macosx_10_9_x86_64.whl (151.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 151.0/151.0 MB 35.9 MB/s 0:00:04 Collecting tqdm (from -r requirements.txt (line 94)) Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) Collecting transforms3d (from -r requirements.txt (line 95)) Downloading transforms3d-0.4.2-py3-none-any.whl.metadata (2.8 kB) Collecting urllib3 (from -r requirements.txt (line 96)) Downloading urllib3-2.6.0-py3-none-any.whl.metadata (6.6 kB) Collecting pytest_console_scripts (from -r requirements.txt (line 97)) Using cached pytest_console_scripts-1.4.1-py3-none-any.whl.metadata (11 kB) Collecting pyyaml (from -r requirements.txt (line 98)) Downloading pyyaml-6.0.3-cp310-cp310-macosx_10_13_x86_64.whl.metadata (2.4 kB) Collecting voxelmorph (from -r requirements.txt (line 99)) Using cached voxelmorph-0.2-py3-none-any.whl.metadata (660 bytes) Collecting wquantiles (from -r requirements.txt (line 100)) Using cached wquantiles-0.6-py3-none-any.whl.metadata (1.1 kB) Collecting xlsxwriter (from -r requirements.txt (line 103)) Downloading xlsxwriter-3.2.9-py3-none-any.whl.metadata (2.7 kB) Collecting monai[nibabel] (from -r requirements.txt (line 27)) Downloading monai-1.5.1-py3-none-any.whl.metadata (13 kB) Collecting totalspineseg[neuropoly] (from -r requirements.txt (line 80)) Downloading totalspineseg-20251124-py3-none-any.whl.metadata (17 kB) Collecting cython!=0.29.29,>=0.29.24 (from dipy==1.8.0->-r requirements.txt (line 14)) Using cached cython-3.2.2-cp39-abi3-macosx_10_9_x86_64.whl.metadata (5.0 kB) Collecting packaging>=21 (from dipy==1.8.0->-r requirements.txt (line 14)) Downloading packaging-25.0-py3-none-any.whl.metadata (3.3 kB) Collecting trx-python>=0.2.9 (from dipy==1.8.0->-r requirements.txt (line 14)) Downloading trx_python-0.3-py3-none-any.whl.metadata (2.7 kB) Collecting coloredlogs (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 55)) Using cached coloredlogs-15.0.1-py2.py3-none-any.whl.metadata (12 kB) Collecting flatbuffers (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 55)) Using cached flatbuffers-25.9.23-py2.py3-none-any.whl.metadata (875 bytes) Collecting protobuf (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 55)) Downloading protobuf-6.33.2-cp39-abi3-macosx_10_9_universal2.whl.metadata (593 bytes) Collecting sympy (from onnxruntime!=1.16.0,<1.22.0,>=1.7.0->-r requirements.txt (line 55)) Downloading https://download.pytorch.org/whl/sympy-1.14.0-py3-none-any.whl.metadata (12 kB) Collecting filelock (from torch<2.3->-r requirements.txt (line 93)) Using cached filelock-3.20.0-py3-none-any.whl.metadata (2.1 kB) Collecting typing-extensions>=4.8.0 (from torch<2.3->-r requirements.txt (line 93)) Downloading https://download.pytorch.org/whl/typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB) Collecting networkx (from torch<2.3->-r requirements.txt (line 93)) Downloading https://download.pytorch.org/whl/networkx-3.5-py3-none-any.whl.metadata (6.3 kB) Collecting jinja2 (from torch<2.3->-r requirements.txt (line 93)) Using cached https://download.pytorch.org/whl/jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB) Collecting fsspec (from torch<2.3->-r requirements.txt (line 93)) Using cached fsspec-2025.12.0-py3-none-any.whl.metadata (10 kB) Collecting batchgenerators (from acvl_utils!=0.2.1->-r requirements.txt (line 7)) Using cached batchgenerators-0.25.1.tar.gz (76 kB) 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' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting SimpleITK (from acvl_utils!=0.2.1->-r requirements.txt (line 7)) Downloading simpleitk-2.5.3-cp310-cp310-macosx_10_9_x86_64.whl.metadata (7.2 kB) Collecting connected-components-3d (from acvl_utils!=0.2.1->-r requirements.txt (line 7)) Using cached connected_components_3d-3.26.1-cp310-cp310-macosx_10_9_x86_64.whl.metadata (32 kB) Collecting ndindex (from blosc2!=3.9.0->-r requirements.txt (line 12)) Using 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joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB) Collecting pandas (from -r requirements.txt (line 59)) Downloading pandas-1.5.3-cp310-cp310-macosx_10_9_x86_64.whl.metadata (11 kB) Collecting pybids<0.15.6,>=0.14.0 (from ivadomed->-r requirements.txt (line 20)) Using cached pybids-0.15.5-py3-none-any.whl.metadata (3.2 kB) Collecting seaborn~=0.11 (from ivadomed->-r requirements.txt (line 20)) Using cached seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) Collecting tensorboard>=1.15.0 (from ivadomed->-r requirements.txt (line 20)) Downloading tensorboard-2.20.0-py3-none-any.whl.metadata (1.8 kB) Collecting torchio>=0.18.68 (from ivadomed->-r requirements.txt (line 20)) Downloading torchio-0.21.0-py3-none-any.whl.metadata (52 kB) Collecting torchvision>=0.9.1 (from ivadomed->-r requirements.txt (line 20)) Downloading https://download.pytorch.org/whl/cpu/torchvision-0.17.2-cp310-cp310-macosx_10_13_x86_64.whl (1.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 19.5 MB/s 0:00:00 Collecting wandb>=0.12.11 (from ivadomed->-r requirements.txt (line 20)) Downloading wandb-0.23.1.tar.gz (44.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.3/44.3 MB 30.5 MB/s 0:00:01 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' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'error' error: subprocess-exited-with-error × Preparing metadata (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [2 lines of output] Building wandb-core Go binary... Did not find the 'go' binary. You need Go to build wandb from source. See https://go.dev/doc/install. [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. ╰─> wandb note: This is an issue with the package mentioned above, not pip. hint: See above for details. Failed running pip install: 1 Installation failed! Please find the file "/Users/msresearch/Downloads/spinalcordtoolbox/install_sct_log.txt", then upload it as a .txt attachment in a new topic on SCT's forum: --> https://forum.spinalcordmri.org/c/sct