Full verbose!
+ getopts :iydbcvh opt
+ trap detectKeyboardInterrupt INT
+ trap finish EXIT
+ print info '
*******************************
* Welcome to SCT installation *
*******************************
'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32m
*******************************
* Welcome to SCT installation *
*******************************
\033[0m\n'


*******************************
* Welcome to SCT installation *
*******************************


+ fetch_os_type
+ print info 'Checking OS type and version...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mChecking OS type and version...\033[0m\n'

Checking OS type and version...

+ OSver=unknown
++ uname -a
+ uname_output='Darwin nesh4tgl0yfpn7c.hsc.net.ou.edu 20.6.0 Darwin Kernel Version 20.6.0: Tue Oct 12 18:33:42 PDT 2021; root:xnu-7195.141.8~1/RELEASE_X86_64 x86_64'
+ echo 'Darwin nesh4tgl0yfpn7c.hsc.net.ou.edu 20.6.0 Darwin Kernel Version 20.6.0: Tue Oct 12 18:33:42 PDT 2021; root:xnu-7195.141.8~1/RELEASE_X86_64 x86_64'
Darwin nesh4tgl0yfpn7c.hsc.net.ou.edu 20.6.0 Darwin Kernel Version 20.6.0: Tue Oct 12 18:33:42 PDT 2021; root:xnu-7195.141.8~1/RELEASE_X86_64 x86_64
+ echo 'Darwin nesh4tgl0yfpn7c.hsc.net.ou.edu 20.6.0 Darwin Kernel Version 20.6.0: Tue Oct 12 18:33:42 PDT 2021; root:xnu-7195.141.8~1/RELEASE_X86_64 x86_64'
+ grep -i darwin
++ sw_vers
++ grep -e ProductVersion
+ sw_vers_output='ProductVersion:	11.6.1'
+ echo 'ProductVersion:	11.6.1'
ProductVersion:	11.6.1
++ echo 'ProductVersion:	11.6.1'
++ cut -c 17-
+ OSver=11.6.1
++ echo 11.6.1
++ cut -f 1 -d .
+ macOSmajor=11
++ echo 11.6.1
++ cut -f 2 -d .
+ macOSminor=6
+ [[ 11 = 10 ]]
+ [[ -z '' ]]
+ export LC_ALL=en_US.UTF-8
+ LC_ALL=en_US.UTF-8
+ [[ -z en_US.UTF-8 ]]
+ OS=osx
+ force_bashrc_loading
+ sourceblock='
if [[ -n "$BASH_VERSION" ]]; then
    # include .bashrc if it exists
    if [[ -f "$HOME/.bashrc" ]]; then
    . "$HOME/.bashrc"
    fi
fi'
+ bidon=
+ for profile in '~/.bash_profile' '~/.bash_login' '~/.profile'
+ [[ -a /Users/Fmuhamma/.bash_profile ]]
+ grep -E '(\.|source) .*bashrc' /Users/Fmuhamma/.bash_profile
+ bidon=done
+ break
+ [[ -z done ]]
+ check_requirements
+ print info 'Checking requirements...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mChecking requirements...\033[0m\n'

Checking requirements...

++ command -v curl
+ [[ -n /usr/bin/curl ]]
+ gcc --version
+ print info 'OK!'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mOK!\033[0m\n'

OK!

+ [[ -e spinalcordtoolbox/version.txt ]]
++ cat spinalcordtoolbox/version.txt
+ SCT_VERSION=5.6
+ [[ -z '' ]]
+ [[ -e requirements-freeze.txt ]]
+ SCT_INSTALL_TYPE=package
+ get_shell_rc_path
+ [[ /bin/bash == *\b\a\s\h* ]]
+ THE_RC=bash
+ RC_FILE_PATH=/Users/Fmuhamma/.bashrc
+ echo -e '\nSCT version ......... 5.6'

SCT version ......... 5.6
+ echo -e 'Installation type ... package'
Installation type ... package
+ echo -e 'Operating system .... osx (11.6.1)'
Operating system .... osx (11.6.1)
+ echo -e 'Shell config ........ /Users/Fmuhamma/.bashrc'
Shell config ........ /Users/Fmuhamma/.bashrc
+ REPORT_STATS=no
+ '[' -z '' ']'
+ print question 'To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: '
+ type=question
+ shift
+ case "$type" in
+ echo -e -n '\n\033[0;92mTo improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: \033[0m'

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: + read -r REPORT_STATS
+ [[ y =~ [Yy](es)? ]]
+ echo -ne '# Auto-generated by install_sct\nimport os\nSENTRY_DSN=os.environ.get("SCT_SENTRY_DSN", "https://5202d7c96ad84f17a24bd2653f1c4f9e:c1394bb176cc426caf0ff6a9095fb955@sentry.io/415369")\n'
+ print info '--> Crash reports will be sent to the SCT development team. Thank you!'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32m--> Crash reports will be sent to the SCT development team. Thank you!\033[0m\n'

--> Crash reports will be sent to the SCT development team. Thank you!

+ [[ package == \i\n\-\p\l\a\c\e ]]
+ SCT_DIR=/Users/Fmuhamma/sct_5.6
+ true
+ keep_default_path=
+ [[ ! '' =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ print info 'SCT will be installed here: [/Users/Fmuhamma/sct_5.6]'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mSCT will be installed here: [/Users/Fmuhamma/sct_5.6]\033[0m\n'

SCT will be installed here: [/Users/Fmuhamma/sct_5.6]

+ keep_default_path=yes
+ '[' -z '' ']'
+ print question '
Do you agree? [y]es/[n]o: '
+ type=question
+ shift
+ case "$type" in
+ echo -e -n '\n\033[0;92m
Do you agree? [y]es/[n]o: \033[0m'


Do you agree? [y]es/[n]o: + read -r keep_default_path
+ [[ ! y =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ [[ y =~ ^[Yy] ]]
+ break
+ space_regex='[[:space:]]+'
+ [[ /Users/Fmuhamma/sct_5.6 =~ [[:space:]]+ ]]
+ add_to_path=
+ [[ ! '' =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ add_to_path=yes
+ '[' -z '' ']'
+ print question 'Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: '
+ type=question
+ shift
+ case "$type" in
+ echo -e -n '\n\033[0;92mDo you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: \033[0m'

Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: + read -r add_to_path
+ [[ ! y =~ ^([Yy](es)?|[Nn]o?)$ ]]
+ mkdir -p /Users/Fmuhamma/sct_5.6
+ [[ -d /Users/Fmuhamma/sct_5.6 ]]
+ [[ ! -w /Users/Fmuhamma/sct_5.6 ]]
+ [[ bash == \b\a\s\h ]]
+ DISPLAY_UPDATE_PATH='export PATH="/Users/Fmuhamma/sct_5.6/bin:$PATH"'
+ [[ /Users/Fmuhamma/sct_5.6 != \/\U\s\e\r\s\/\F\m\u\h\a\m\m\a\/\D\o\w\n\l\o\a\d\s\/\s\p\i\n\a\l\c\o\r\d\t\o\o\l\b\o\x\-\5\.\6 ]]
+ print info 'Copying source files from /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6 to /Users/Fmuhamma/sct_5.6'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mCopying source files from /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6 to /Users/Fmuhamma/sct_5.6\033[0m\n'

Copying source files from /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6 to /Users/Fmuhamma/sct_5.6

+ read -r
+ cp -vR /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/CHANGES.md /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/CODE_OF_CONDUCT.md /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/CONTRIBUTING.rst /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/LICENSE /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/MANIFEST.in /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/README.rst /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/batch_processing.sh /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/codecov.yml /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/contrib /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/dev /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/documentation /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/install_sct /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/install_sct.bat /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/install_sct_debug /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/install_sct_log.txt /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/patches /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/requirements-freeze.txt /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/requirements.txt /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/setup.cfg /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/setup.py /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/spinalcordtoolbox /Users/Fmuhamma/Downloads/spinalcordtoolbox-5.6/testing /Users/Fmuhamma/sct_5.6/
+ echo -n .
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+ [[ -x /Users/Fmuhamma/sct_5.6/bin ]]
+ cd /Users/Fmuhamma/sct_5.6
+ [[ ! -f spinalcordtoolbox/version.txt ]]
+ run rm -rf /Users/Fmuhamma/sct_5.6/python
+ print code rm -rf /Users/Fmuhamma/sct_5.6/python
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mrm -rf /Users/Fmuhamma/sct_5.6/python\033[0m\n'

rm -rf /Users/Fmuhamma/sct_5.6/python

+ rm -rf /Users/Fmuhamma/sct_5.6/python
+ run mkdir -p /Users/Fmuhamma/sct_5.6/python
+ print code mkdir -p /Users/Fmuhamma/sct_5.6/python
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mmkdir -p /Users/Fmuhamma/sct_5.6/python\033[0m\n'

mkdir -p /Users/Fmuhamma/sct_5.6/python

+ mkdir -p /Users/Fmuhamma/sct_5.6/python
+ print info 'Downloading Miniconda...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mDownloading Miniconda...\033[0m\n'

Downloading Miniconda...

+ case $OS in
+ download /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
+ command -v wget
+ command -v curl
+ run curl -sS -o /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
+ print code curl -sS -o /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mcurl -sS -o /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh\033[0m\n'

curl -sS -o /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

+ curl -sS -o /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
+ print info 'Installing Miniconda...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling Miniconda...\033[0m\n'

Installing Miniconda...

+ run bash /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -p /Users/Fmuhamma/sct_5.6/python -b -f
+ print code bash /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -p /Users/Fmuhamma/sct_5.6/python -b -f
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mbash /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -p /Users/Fmuhamma/sct_5.6/python -b -f\033[0m\n'

bash /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -p /Users/Fmuhamma/sct_5.6/python -b -f

+ bash /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63/miniconda.sh -p /Users/Fmuhamma/sct_5.6/python -b -f
PREFIX=/Users/Fmuhamma/sct_5.6/python
Unpacking payload ...

  0%|          | 0/36 [00:00<?, ?it/s]
Extracting : cffi-1.15.0-py39hc55c11b_1.conda:   0%|          | 0/36 [00:00<?, ?it/s]
Extracting : cffi-1.15.0-py39hc55c11b_1.conda:   3%|▎         | 1/36 [00:00<00:12,  2.82it/s]
Extracting : openssl-1.1.1n-hca72f7f_0.conda:   3%|▎         | 1/36 [00:00<00:12,  2.82it/s] 
Extracting : openssl-1.1.1n-hca72f7f_0.conda:   6%|▌         | 2/36 [00:00<00:09,  3.48it/s]
Extracting : certifi-2021.10.8-py39hecd8cb5_2.conda:   6%|▌         | 2/36 [00:00<00:09,  3.48it/s]
Extracting : conda-package-handling-1.8.1-py39hca72f7f_0.conda:   8%|▊         | 3/36 [00:00<00:09,  3.48it/s]
Extracting : libffi-3.3-hb1e8313_2.conda:  11%|█         | 4/36 [00:00<00:09,  3.48it/s]                      
Extracting : ruamel_yaml-0.15.100-py39h9ed2024_0.conda:  14%|█▍        | 5/36 [00:00<00:08,  3.48it/s]
Extracting : requests-2.27.1-pyhd3eb1b0_0.conda:  17%|█▋        | 6/36 [00:00<00:08,  3.48it/s]       
Extracting : ca-certificates-2022.3.29-hecd8cb5_1.conda:  19%|█▉        | 7/36 [00:00<00:08,  3.48it/s]
Extracting : pysocks-1.7.1-py39hecd8cb5_0.conda:  22%|██▏       | 8/36 [00:00<00:08,  3.48it/s]        
Extracting : zlib-1.2.12-h4dc903c_1.conda:  25%|██▌       | 9/36 [00:00<00:07,  3.48it/s]      
Extracting : six-1.16.0-pyhd3eb1b0_1.conda:  28%|██▊       | 10/36 [00:00<00:07,  3.48it/s]
Extracting : ncurses-6.3-hca72f7f_2.conda:  31%|███       | 11/36 [00:01<00:07,  3.48it/s] 
Extracting : ncurses-6.3-hca72f7f_2.conda:  33%|███▎      | 12/36 [00:01<00:03,  6.96it/s]
Extracting : colorama-0.4.4-pyhd3eb1b0_0.conda:  33%|███▎      | 12/36 [00:01<00:03,  6.96it/s]
Extracting : wheel-0.37.1-pyhd3eb1b0_0.conda:  36%|███▌      | 13/36 [00:01<00:03,  6.96it/s]  
Extracting : brotlipy-0.7.0-py39h9ed2024_1003.conda:  39%|███▉      | 14/36 [00:01<00:03,  6.96it/s]
Extracting : charset-normalizer-2.0.4-pyhd3eb1b0_0.conda:  42%|████▏     | 15/36 [00:01<00:03,  6.96it/s]
Extracting : tk-8.6.11-h7bc2e8c_0.conda:  44%|████▍     | 16/36 [00:01<00:02,  6.96it/s]                 
Extracting : pycosat-0.6.3-py39h9ed2024_0.conda:  47%|████▋     | 17/36 [00:01<00:02,  6.96it/s]
Extracting : sqlite-3.38.2-h707629a_0.conda:  50%|█████     | 18/36 [00:01<00:02,  6.96it/s]    
Extracting : readline-8.1.2-hca72f7f_1.conda:  53%|█████▎    | 19/36 [00:01<00:02,  6.96it/s]
Extracting : pycparser-2.21-pyhd3eb1b0_0.conda:  56%|█████▌    | 20/36 [00:01<00:02,  6.96it/s]
Extracting : python-3.9.12-hdfd78df_0.conda:  58%|█████▊    | 21/36 [00:01<00:02,  6.96it/s]   
Extracting : pyopenssl-22.0.0-pyhd3eb1b0_0.conda:  61%|██████    | 22/36 [00:01<00:02,  6.96it/s]
Extracting : pip-21.2.4-py39hecd8cb5_0.conda:  64%|██████▍   | 23/36 [00:01<00:01,  6.96it/s]    
Extracting : conda-4.12.0-py39hecd8cb5_0.conda:  67%|██████▋   | 24/36 [00:02<00:01,  6.96it/s]
Extracting : conda-4.12.0-py39hecd8cb5_0.conda:  69%|██████▉   | 25/36 [00:02<00:00, 13.73it/s]
Extracting : cryptography-36.0.0-py39hf6deb26_0.conda:  69%|██████▉   | 25/36 [00:02<00:00, 13.73it/s]
Extracting : urllib3-1.26.8-pyhd3eb1b0_0.conda:  72%|███████▏  | 26/36 [00:02<00:00, 13.73it/s]       
Extracting : python.app-3-py39hca72f7f_0.conda:  75%|███████▌  | 27/36 [00:02<00:00, 13.73it/s]
Extracting : conda-content-trust-0.1.1-pyhd3eb1b0_0.conda:  78%|███████▊  | 28/36 [00:02<00:00, 13.73it/s]
Extracting : idna-3.3-pyhd3eb1b0_0.conda:  81%|████████  | 29/36 [00:02<00:00, 13.73it/s]                 
Extracting : tzdata-2022a-hda174b7_0.conda:  83%|████████▎ | 30/36 [00:02<00:00, 13.73it/s]
Extracting : xz-5.2.5-h1de35cc_0.conda:  86%|████████▌ | 31/36 [00:02<00:00, 13.73it/s]    
Extracting : libcxx-12.0.0-h2f01273_0.conda:  89%|████████▉ | 32/36 [00:02<00:00, 13.73it/s]
Extracting : yaml-0.2.5-haf1e3a3_0.conda:  92%|█████████▏| 33/36 [00:02<00:00, 13.73it/s]   
Extracting : tqdm-4.63.0-pyhd3eb1b0_0.conda:  94%|█████████▍| 34/36 [00:02<00:00, 13.73it/s]
Extracting : setuptools-61.2.0-py39hecd8cb5_0.conda:  97%|█████████▋| 35/36 [00:02<00:00, 13.73it/s]
                                                                                                    
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/Fmuhamma/sct_5.6/python

  added / updated specs:
    - brotlipy==0.7.0=py39h9ed2024_1003
    - ca-certificates==2022.3.29=hecd8cb5_1
    - certifi==2021.10.8=py39hecd8cb5_2
    - cffi==1.15.0=py39hc55c11b_1
    - charset-normalizer==2.0.4=pyhd3eb1b0_0
    - colorama==0.4.4=pyhd3eb1b0_0
    - conda-content-trust==0.1.1=pyhd3eb1b0_0
    - conda-package-handling==1.8.1=py39hca72f7f_0
    - conda==4.12.0=py39hecd8cb5_0
    - cryptography==36.0.0=py39hf6deb26_0
    - idna==3.3=pyhd3eb1b0_0
    - libcxx==12.0.0=h2f01273_0
    - libffi==3.3=hb1e8313_2
    - ncurses==6.3=hca72f7f_2
    - openssl==1.1.1n=hca72f7f_0
    - pip==21.2.4=py39hecd8cb5_0
    - pycosat==0.6.3=py39h9ed2024_0
    - pycparser==2.21=pyhd3eb1b0_0
    - pyopenssl==22.0.0=pyhd3eb1b0_0
    - pysocks==1.7.1=py39hecd8cb5_0
    - python.app==3=py39hca72f7f_0
    - python==3.9.12=hdfd78df_0
    - readline==8.1.2=hca72f7f_1
    - requests==2.27.1=pyhd3eb1b0_0
    - ruamel_yaml==0.15.100=py39h9ed2024_0
    - setuptools==61.2.0=py39hecd8cb5_0
    - six==1.16.0=pyhd3eb1b0_1
    - sqlite==3.38.2=h707629a_0
    - tk==8.6.11=h7bc2e8c_0
    - tqdm==4.63.0=pyhd3eb1b0_0
    - tzdata==2022a=hda174b7_0
    - urllib3==1.26.8=pyhd3eb1b0_0
    - wheel==0.37.1=pyhd3eb1b0_0
    - xz==5.2.5=h1de35cc_0
    - yaml==0.2.5=haf1e3a3_0
    - zlib==1.2.12=h4dc903c_1


The following NEW packages will be INSTALLED:

  brotlipy           pkgs/main/osx-64::brotlipy-0.7.0-py39h9ed2024_1003
  ca-certificates    pkgs/main/osx-64::ca-certificates-2022.3.29-hecd8cb5_1
  certifi            pkgs/main/osx-64::certifi-2021.10.8-py39hecd8cb5_2
  cffi               pkgs/main/osx-64::cffi-1.15.0-py39hc55c11b_1
  charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
  colorama           pkgs/main/noarch::colorama-0.4.4-pyhd3eb1b0_0
  conda              pkgs/main/osx-64::conda-4.12.0-py39hecd8cb5_0
  conda-content-tru~ pkgs/main/noarch::conda-content-trust-0.1.1-pyhd3eb1b0_0
  conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.8.1-py39hca72f7f_0
  cryptography       pkgs/main/osx-64::cryptography-36.0.0-py39hf6deb26_0
  idna               pkgs/main/noarch::idna-3.3-pyhd3eb1b0_0
  libcxx             pkgs/main/osx-64::libcxx-12.0.0-h2f01273_0
  libffi             pkgs/main/osx-64::libffi-3.3-hb1e8313_2
  ncurses            pkgs/main/osx-64::ncurses-6.3-hca72f7f_2
  openssl            pkgs/main/osx-64::openssl-1.1.1n-hca72f7f_0
  pip                pkgs/main/osx-64::pip-21.2.4-py39hecd8cb5_0
  pycosat            pkgs/main/osx-64::pycosat-0.6.3-py39h9ed2024_0
  pycparser          pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
  pyopenssl          pkgs/main/noarch::pyopenssl-22.0.0-pyhd3eb1b0_0
  pysocks            pkgs/main/osx-64::pysocks-1.7.1-py39hecd8cb5_0
  python             pkgs/main/osx-64::python-3.9.12-hdfd78df_0
  python.app         pkgs/main/osx-64::python.app-3-py39hca72f7f_0
  readline           pkgs/main/osx-64::readline-8.1.2-hca72f7f_1
  requests           pkgs/main/noarch::requests-2.27.1-pyhd3eb1b0_0
  ruamel_yaml        pkgs/main/osx-64::ruamel_yaml-0.15.100-py39h9ed2024_0
  setuptools         pkgs/main/osx-64::setuptools-61.2.0-py39hecd8cb5_0
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
  sqlite             pkgs/main/osx-64::sqlite-3.38.2-h707629a_0
  tk                 pkgs/main/osx-64::tk-8.6.11-h7bc2e8c_0
  tqdm               pkgs/main/noarch::tqdm-4.63.0-pyhd3eb1b0_0
  tzdata             pkgs/main/noarch::tzdata-2022a-hda174b7_0
  urllib3            pkgs/main/noarch::urllib3-1.26.8-pyhd3eb1b0_0
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  yaml               pkgs/main/osx-64::yaml-0.2.5-haf1e3a3_0
  zlib               pkgs/main/osx-64::zlib-1.2.12-h4dc903c_1


Preparing transaction: ...working... done
Executing transaction: ...working... 
done
installation finished.
+ find /Users/Fmuhamma/sct_5.6/python -type f -exec touch '{}' +
+ print info 'Creating conda environment...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mCreating conda environment...\033[0m\n'

Creating conda environment...

+ python/bin/conda create -y -n venv_sct python=3.7
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /Users/Fmuhamma/sct_5.6/python/envs/venv_sct

  added / updated specs:
    - python=3.7


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.4.26  |       hecd8cb5_0         124 KB
    certifi-2022.5.18.1        |   py37hecd8cb5_0         148 KB
    openssl-1.1.1o             |       hca72f7f_0         2.2 MB
    pip-21.2.2                 |   py37hecd8cb5_0         1.8 MB
    python-3.7.13              |       hdfd78df_0        20.3 MB
    setuptools-61.2.0          |   py37hecd8cb5_0        1008 KB
    sqlite-3.38.3              |       h707629a_0         1.2 MB
    tk-8.6.11                  |       h3fd3227_1         3.0 MB
    xz-5.2.5                   |       hca72f7f_1         244 KB
    zlib-1.2.12                |       h4dc903c_2          94 KB
    ------------------------------------------------------------
                                           Total:        30.1 MB

The following NEW packages will be INSTALLED:

  ca-certificates    pkgs/main/osx-64::ca-certificates-2022.4.26-hecd8cb5_0
  certifi            pkgs/main/osx-64::certifi-2022.5.18.1-py37hecd8cb5_0
  libcxx             pkgs/main/osx-64::libcxx-12.0.0-h2f01273_0
  libffi             pkgs/main/osx-64::libffi-3.3-hb1e8313_2
  ncurses            pkgs/main/osx-64::ncurses-6.3-hca72f7f_2
  openssl            pkgs/main/osx-64::openssl-1.1.1o-hca72f7f_0
  pip                pkgs/main/osx-64::pip-21.2.2-py37hecd8cb5_0
  python             pkgs/main/osx-64::python-3.7.13-hdfd78df_0
  readline           pkgs/main/osx-64::readline-8.1.2-hca72f7f_1
  setuptools         pkgs/main/osx-64::setuptools-61.2.0-py37hecd8cb5_0
  sqlite             pkgs/main/osx-64::sqlite-3.38.3-h707629a_0
  tk                 pkgs/main/osx-64::tk-8.6.11-h3fd3227_1
  wheel              pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
  xz                 pkgs/main/osx-64::xz-5.2.5-hca72f7f_1
  zlib               pkgs/main/osx-64::zlib-1.2.12-h4dc903c_2



Downloading and Extracting Packages

sqlite-3.38.3        | 1.2 MB    |            |   0% 
sqlite-3.38.3        | 1.2 MB    | ########3  |  83% 
sqlite-3.38.3        | 1.2 MB    | ########## | 100% 

pip-21.2.2           | 1.8 MB    |            |   0% 
pip-21.2.2           | 1.8 MB    | ########## | 100% 
pip-21.2.2           | 1.8 MB    | ########## | 100% 

xz-5.2.5             | 244 KB    |            |   0% 
xz-5.2.5             | 244 KB    | ########## | 100% 

ca-certificates-2022 | 124 KB    |            |   0% 
ca-certificates-2022 | 124 KB    | ########## | 100% 

certifi-2022.5.18.1  | 148 KB    |            |   0% 
certifi-2022.5.18.1  | 148 KB    | ########## | 100% 
certifi-2022.5.18.1  | 148 KB    | ########## | 100% 

openssl-1.1.1o       | 2.2 MB    |            |   0% 
openssl-1.1.1o       | 2.2 MB    | ########## | 100% 
openssl-1.1.1o       | 2.2 MB    | ########## | 100% 

setuptools-61.2.0    | 1008 KB   |            |   0% 
setuptools-61.2.0    | 1008 KB   | ########## | 100% 
setuptools-61.2.0    | 1008 KB   | ########## | 100% 

zlib-1.2.12          | 94 KB     |            |   0% 
zlib-1.2.12          | 94 KB     | ########## | 100% 

python-3.7.13        | 20.3 MB   |            |   0% 
python-3.7.13        | 20.3 MB   | ##9        |  29% 
python-3.7.13        | 20.3 MB   | ########6  |  86% 
python-3.7.13        | 20.3 MB   | ########## | 100% 

tk-8.6.11            | 3.0 MB    |            |   0% 
tk-8.6.11            | 3.0 MB    | ########## | 100% 
tk-8.6.11            | 3.0 MB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

+ find /Users/Fmuhamma/sct_5.6/python -type f -exec touch '{}' +
+ echo 'include-system-site-packages = false'
+ source python/etc/profile.d/conda.sh
++ export CONDA_EXE=/Users/Fmuhamma/sct_5.6/python/bin/conda
++ CONDA_EXE=/Users/Fmuhamma/sct_5.6/python/bin/conda
++ export _CE_M=
++ _CE_M=
++ export _CE_CONDA=
++ _CE_CONDA=
++ export CONDA_PYTHON_EXE=/Users/Fmuhamma/sct_5.6/python/bin/python
++ CONDA_PYTHON_EXE=/Users/Fmuhamma/sct_5.6/python/bin/python
++ '[' -z '' ']'
++ export CONDA_SHLVL=0
++ CONDA_SHLVL=0
++ '[' -n '' ']'
++++ dirname /Users/Fmuhamma/sct_5.6/python/bin/conda
+++ dirname /Users/Fmuhamma/sct_5.6/python/bin
++ PATH=/Users/Fmuhamma/sct_5.6/python/condabin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
++ export PATH
++ '[' -z '' ']'
++ PS1=
+ set +u
+ conda activate venv_sct
+ local cmd=activate
+ case "$cmd" in
+ __conda_activate activate venv_sct
+ '[' -n '' ']'
+ local ask_conda
++ PS1=
++ __conda_exe shell.posix activate venv_sct
++ __add_sys_prefix_to_path
++ '[' -n '' ']'
+++ dirname /Users/Fmuhamma/sct_5.6/python/bin/conda
++ SYSP=/Users/Fmuhamma/sct_5.6/python/bin
+++ dirname /Users/Fmuhamma/sct_5.6/python/bin
++ SYSP=/Users/Fmuhamma/sct_5.6/python
++ '[' -n '' ']'
++ PATH=/Users/Fmuhamma/sct_5.6/python/bin:/Users/Fmuhamma/sct_5.6/python/condabin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
++ export PATH
++ /Users/Fmuhamma/sct_5.6/python/bin/conda shell.posix activate venv_sct
+ ask_conda='PS1='\''(venv_sct) '\''
export PATH='\''/Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin:/Users/Fmuhamma/sct_5.6/python/condabin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin'\''
export CONDA_PREFIX='\''/Users/Fmuhamma/sct_5.6/python/envs/venv_sct'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''venv_sct'\''
export CONDA_PROMPT_MODIFIER='\''(venv_sct) '\''
export CONDA_EXE='\''/Users/Fmuhamma/sct_5.6/python/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/Users/Fmuhamma/sct_5.6/python/bin/python'\'''
+ eval 'PS1='\''(venv_sct) '\''
export PATH='\''/Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin:/Users/Fmuhamma/sct_5.6/python/condabin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin'\''
export CONDA_PREFIX='\''/Users/Fmuhamma/sct_5.6/python/envs/venv_sct'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''venv_sct'\''
export CONDA_PROMPT_MODIFIER='\''(venv_sct) '\''
export CONDA_EXE='\''/Users/Fmuhamma/sct_5.6/python/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/Users/Fmuhamma/sct_5.6/python/bin/python'\'''
++ PS1='(venv_sct) '
++ export PATH=/Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin:/Users/Fmuhamma/sct_5.6/python/condabin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
++ PATH=/Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin:/Users/Fmuhamma/sct_5.6/python/condabin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
++ export CONDA_PREFIX=/Users/Fmuhamma/sct_5.6/python/envs/venv_sct
++ CONDA_PREFIX=/Users/Fmuhamma/sct_5.6/python/envs/venv_sct
++ export CONDA_SHLVL=1
++ CONDA_SHLVL=1
++ export CONDA_DEFAULT_ENV=venv_sct
++ CONDA_DEFAULT_ENV=venv_sct
++ export 'CONDA_PROMPT_MODIFIER=(venv_sct) '
++ CONDA_PROMPT_MODIFIER='(venv_sct) '
++ export CONDA_EXE=/Users/Fmuhamma/sct_5.6/python/bin/conda
++ CONDA_EXE=/Users/Fmuhamma/sct_5.6/python/bin/conda
++ export _CE_M=
++ _CE_M=
++ export _CE_CONDA=
++ _CE_CONDA=
++ export CONDA_PYTHON_EXE=/Users/Fmuhamma/sct_5.6/python/bin/python
++ CONDA_PYTHON_EXE=/Users/Fmuhamma/sct_5.6/python/bin/python
+ __conda_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ set -u
+ print info 'Validating that conda environment can be activated...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mValidating that conda environment can be activated...\033[0m\n'

Validating that conda environment can be activated...

+++ command -v python/envs/venv_sct/bin/python
++ realpath python/envs/venv_sct/bin/python
++ python3 -c 'import sys, os; [print(os.path.realpath(f)) for f in sys.argv[1:]]' python/envs/venv_sct/bin/python
+ EXPECTED_PYTHON=/Users/fmuhamma/sct_5.6/python/envs/venv_sct/bin/python3.7
+++ command -v python
++ realpath /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/python
++ python3 -c 'import sys, os; [print(os.path.realpath(f)) for f in sys.argv[1:]]' /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/python
+ ACTUAL_PYTHON=/Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/python3.7
+ '[' /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/python3.7 '!=' /Users/fmuhamma/sct_5.6/python/envs/venv_sct/bin/python3.7 ']'
+ echo 'Mismatch between expected and actual python!'
Mismatch between expected and actual python!
+ pwd
/Users/Fmuhamma/sct_5.6
+ echo 'Expected Python: /Users/fmuhamma/sct_5.6/python/envs/venv_sct/bin/python3.7'
Expected Python: /Users/fmuhamma/sct_5.6/python/envs/venv_sct/bin/python3.7
+ echo 'Actual Python: /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/python3.7'
Actual Python: /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/python3.7
+ python -m pip install -U 'pip!=21.2.*'
Collecting pip!=21.2.*
  Downloading pip-22.1.1-py3-none-any.whl (2.1 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 21.2.2
    Uninstalling pip-21.2.2:
      Successfully uninstalled pip-21.2.2
Successfully installed pip-22.1.1
+ print info 'Installing Python dependencies...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling Python dependencies...\033[0m\n'

Installing Python dependencies...

+ [[ -f requirements-freeze.txt ]]
+ print info 'Using requirements-freeze.txt (release installation)'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mUsing requirements-freeze.txt (release installation)\033[0m\n'

Using requirements-freeze.txt (release installation)

+ REQUIREMENTS_FILE=requirements-freeze.txt
+ pip install -r requirements-freeze.txt --ignore-installed certifi
Looking in links: https://download.pytorch.org/whl/torch/, https://download.pytorch.org/whl/torchvision/
Ignoring torch: markers 'sys_platform != "darwin"' don't match your environment
Ignoring torchvision: markers 'sys_platform != "darwin"' don't match your environment
Collecting certifi
  Downloading certifi-2022.5.18.1-py3-none-any.whl (155 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.2/155.2 kB 3.7 MB/s eta 0:00:00
Collecting absl-py==1.0.0
  Downloading absl_py-1.0.0-py3-none-any.whl (126 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.7/126.7 kB 4.8 MB/s eta 0:00:00
Collecting astor==0.7.1
  Downloading astor-0.7.1-py2.py3-none-any.whl (27 kB)
Collecting attrs==21.4.0
  Downloading attrs-21.4.0-py2.py3-none-any.whl (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 1.9 MB/s eta 0:00:00
Collecting bids-validator==1.9.3
  Downloading bids_validator-1.9.3-py2.py3-none-any.whl (21 kB)
Collecting certifi
  Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 149.2/149.2 kB 5.2 MB/s eta 0:00:00
Collecting cffi==1.15.0
  Downloading cffi-1.15.0-cp37-cp37m-macosx_10_9_x86_64.whl (178 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 178.6/178.6 kB 6.3 MB/s eta 0:00:00
Collecting charset-normalizer==2.0.12
  Downloading charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
Collecting click==8.1.3
  Downloading click-8.1.3-py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.6/96.6 kB 2.3 MB/s eta 0:00:00
Collecting coverage==6.3.2
  Downloading coverage-6.3.2-cp37-cp37m-macosx_10_9_x86_64.whl (182 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 182.9/182.9 kB 7.3 MB/s eta 0:00:00
Collecting cryptography==37.0.1
  Downloading cryptography-37.0.1-cp36-abi3-macosx_10_10_x86_64.whl (2.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 44.1 MB/s eta 0:00:00
Collecting csv-diff==1.1
  Downloading csv_diff-1.1-py3-none-any.whl (12 kB)
Collecting cycler==0.11.0
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting Deprecated==1.2.13
  Downloading Deprecated-1.2.13-py2.py3-none-any.whl (9.6 kB)
Collecting dictdiffer==0.9.0
  Downloading dictdiffer-0.9.0-py2.py3-none-any.whl (16 kB)
Collecting dipy==1.5.0
  Downloading dipy-1.5.0-cp37-cp37m-macosx_10_9_x86_64.whl (7.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.7/7.7 MB 69.8 MB/s eta 0:00:00
Collecting docopt==0.6.2
  Downloading docopt-0.6.2.tar.gz (25 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting fonttools==4.33.3
  Downloading fonttools-4.33.3-py3-none-any.whl (930 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 930.9/930.9 kB 24.6 MB/s eta 0:00:00
Collecting formulaic==0.3.3
  Downloading formulaic-0.3.3-py3-none-any.whl (56 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.1/56.1 kB 1.7 MB/s eta 0:00:00
Collecting future==0.18.2
  Downloading future-0.18.2.tar.gz (829 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 kB 25.9 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting gast==0.2.2
  Downloading gast-0.2.2.tar.gz (10 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting google-pasta==0.2.0
  Downloading google_pasta-0.2.0-py3-none-any.whl (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.5/57.5 kB 2.0 MB/s eta 0:00:00
Collecting grpcio==1.44.0
  Downloading grpcio-1.44.0-cp37-cp37m-macosx_10_10_x86_64.whl (4.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.2/4.2 MB 60.9 MB/s eta 0:00:00
Collecting h5py==2.10.0
  Downloading h5py-2.10.0-cp37-cp37m-macosx_10_6_intel.whl (3.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 53.6 MB/s eta 0:00:00
Collecting humanize==4.0.0
  Downloading humanize-4.0.0-py3-none-any.whl (97 kB)
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Collecting idna==3.3
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Collecting imageio==2.18.0
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Collecting importlib-metadata==4.11.3
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Collecting iniconfig==1.1.1
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Collecting interface-meta==1.3.0
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Collecting ivadomed==2.9.5
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Collecting joblib==1.1.0
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Collecting Keras==2.3.1
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Collecting Keras-Applications==1.0.8
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Collecting Keras-Preprocessing==1.1.2
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Collecting kiwisolver==1.4.2
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Collecting loguru==0.6.0
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Collecting Markdown==3.3.6
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Collecting matplotlib==3.5.1
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Collecting networkx==2.6.3
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Collecting nibabel==3.2.2
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Collecting num2words==0.5.10
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Collecting numpy==1.18.5
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Collecting onnxruntime==1.7.0
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Collecting opt-einsum==3.3.0
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Collecting packaging==21.3
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Collecting pandas==1.3.5
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Collecting Pillow==9.1.0
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Collecting pluggy==1.0.0
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Collecting portalocker==2.4.0
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Collecting protobuf==3.20.1
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Collecting psutil==5.9.0
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Collecting py==1.11.0
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Collecting pybids==0.15.1
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Collecting pycparser==2.21
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Collecting pyOpenSSL==22.0.0
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Collecting pyparsing==2.4.7
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Collecting PyQt5==5.11.3
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Collecting PyQt5_sip==4.19.19
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Collecting pytest==7.1.2
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Collecting pytest-console-scripts==1.3.1
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Collecting pytest-cov==3.0.0
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Collecting python-dateutil==2.8.2
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Collecting pytz==2022.1
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Collecting PyWavelets==1.3.0
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Collecting PyYAML==6.0
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Collecting raven==6.10.0
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Collecting requests==2.27.1
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Collecting requirements-parser==0.5.0
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Collecting scikit-image==0.19.2
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Collecting scikit-learn==1.0.2
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Collecting scipy==1.7.3
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Collecting seaborn==0.11.2
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Collecting SimpleITK==2.1.1.2
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Collecting six==1.16.0
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Collecting SQLAlchemy==1.3.24
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Collecting tensorboard==1.15.0
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Collecting tensorflow==1.15.5
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Collecting tensorflow-estimator==1.15.1
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Collecting termcolor==1.1.0
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Collecting threadpoolctl==3.1.0
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Collecting tifffile==2021.11.2
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Collecting tomli==2.0.1
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Collecting tqdm==4.64.0
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Collecting transforms3d==0.3.1
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Collecting types-setuptools==57.4.14
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Collecting urllib3==1.26.9
  Downloading urllib3-1.26.9-py2.py3-none-any.whl (138 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.0/139.0 kB 5.3 MB/s eta 0:00:00
Collecting Werkzeug==2.1.2
  Downloading Werkzeug-2.1.2-py3-none-any.whl (224 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 224.9/224.9 kB 8.4 MB/s eta 0:00:00
Collecting wquantiles==0.6
  Downloading wquantiles-0.6-py3-none-any.whl (3.3 kB)
Collecting wrapt==1.14.0
  Downloading wrapt-1.14.0-cp37-cp37m-macosx_10_9_x86_64.whl (34 kB)
Collecting xlwt==1.3.0
  Downloading xlwt-1.3.0-py2.py3-none-any.whl (99 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.0/100.0 kB 3.8 MB/s eta 0:00:00
Collecting zipp==3.8.0
  Downloading zipp-3.8.0-py3-none-any.whl (5.4 kB)
Collecting torch==1.5.0
  Downloading torch-1.5.0-cp37-none-macosx_10_9_x86_64.whl (80.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.5/80.5 MB 42.4 MB/s eta 0:00:00
Collecting torchvision==0.6.0
  Downloading torchvision-0.6.0-cp37-cp37m-macosx_10_9_x86_64.whl (436 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 436.3/436.3 kB 15.0 MB/s eta 0:00:00
Collecting torchio>=0.18.68
  Downloading torchio-0.18.77-py2.py3-none-any.whl (167 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 167.5/167.5 kB 6.3 MB/s eta 0:00:00
Collecting setuptools
  Downloading setuptools-62.3.2-py3-none-any.whl (1.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 36.5 MB/s eta 0:00:00
Collecting coverage[toml]>=5.2.1
  Downloading coverage-6.3.3-cp37-cp37m-macosx_10_9_x86_64.whl (182 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 183.0/183.0 kB 6.4 MB/s eta 0:00:00
Collecting wheel>=0.26
  Downloading wheel-0.37.1-py2.py3-none-any.whl (35 kB)
Building wheels for collected packages: docopt, future, gast, termcolor, transforms3d
  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=13723 sha256=3706a45c20795e4f66536f54cbff2cb3bb3d53ab50856ae09c08efc048731ddd
  Stored in directory: /Users/Fmuhamma/Library/Caches/pip/wheels/72/b0/3f/1d95f96ff986c7dfffe46ce2be4062f38ebd04b506c77c81b9
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=df1cf23615dbb42ffefe5f5e6e70f01c4aaed4cdbbedc0aa258f77fc5a89c670
  Stored in directory: /Users/Fmuhamma/Library/Caches/pip/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
  Building wheel for gast (setup.py): started
  Building wheel for gast (setup.py): finished with status 'done'
  Created wheel for gast: filename=gast-0.2.2-py3-none-any.whl size=7554 sha256=b56e312d5c20e8872aebf3d57002deb0a2e261321a1fc1d118c3c5231611bd0e
  Stored in directory: /Users/Fmuhamma/Library/Caches/pip/wheels/21/7f/02/420f32a803f7d0967b48dd823da3f558c5166991bfd204eef3
  Building wheel for termcolor (setup.py): started
  Building wheel for termcolor (setup.py): finished with status 'done'
  Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4848 sha256=6469f6aa4645337ba6f5675ecc7663c71ce743a34c633d754fe08cdc5474ec94
  Stored in directory: /Users/Fmuhamma/Library/Caches/pip/wheels/3f/e3/ec/8a8336ff196023622fbcb36de0c5a5c218cbb24111d1d4c7f2
  Building wheel for transforms3d (setup.py): started
  Building wheel for transforms3d (setup.py): finished with status 'done'
  Created wheel for transforms3d: filename=transforms3d-0.3.1-py3-none-any.whl size=59373 sha256=a1bbb915cff36c1d09065e0ccf3fc25b9f2642cde8358f0743cbbf15c1275570
  Stored in directory: /Users/Fmuhamma/Library/Caches/pip/wheels/b5/b7/93/8985551f83720ce37548a5b543c75380bb707955a9c2c5d28c
Successfully built docopt future gast termcolor transforms3d
Installing collected packages: xlwt, types-setuptools, transforms3d, termcolor, tensorflow-estimator, SimpleITK, raven, pytz, PyQt5_sip, iniconfig, docopt, dictdiffer, certifi, bids-validator, zipp, wrapt, wheel, Werkzeug, urllib3, typing_extensions, tqdm, tomli, threadpoolctl, SQLAlchemy, six, setuptools, requirements-parser, PyYAML, PyQt5, pyparsing, pycparser, py, psutil, protobuf, portalocker, Pillow, numpy, num2words, networkx, loguru, joblib, interface-meta, idna, gast, future, fonttools, cycler, coverage, charset-normalizer, attrs, astor, wquantiles, torch, tifffile, scipy, requests, PyWavelets, python-dateutil, packaging, opt-einsum, onnxruntime, kiwisolver, Keras-Preprocessing, importlib-metadata, imageio, h5py, grpcio, google-pasta, Deprecated, cffi, absl-py, torchvision, scikit-learn, scikit-image, pluggy, pandas, nibabel, matplotlib, Markdown, Keras-Applications, humanize, cryptography, click, torchio, tensorboard, seaborn, pytest, pyOpenSSL, Keras, formulaic, dipy, csv-diff, tensorflow, pytest-cov, pytest-console-scripts, pybids, ivadomed
Successfully installed Deprecated-1.2.13 Keras-2.3.1 Keras-Applications-1.0.8 Keras-Preprocessing-1.1.2 Markdown-3.3.6 Pillow-9.1.0 PyQt5-5.11.3 PyQt5_sip-4.19.19 PyWavelets-1.3.0 PyYAML-6.0 SQLAlchemy-1.3.24 SimpleITK-2.1.1.2 Werkzeug-2.1.2 absl-py-1.0.0 astor-0.7.1 attrs-21.4.0 bids-validator-1.9.3 certifi-2022.5.18.1 cffi-1.15.0 charset-normalizer-2.0.12 click-8.1.3 coverage-6.3.2 cryptography-37.0.1 csv-diff-1.1 cycler-0.11.0 dictdiffer-0.9.0 dipy-1.5.0 docopt-0.6.2 fonttools-4.33.3 formulaic-0.3.3 future-0.18.2 gast-0.2.2 google-pasta-0.2.0 grpcio-1.44.0 h5py-2.10.0 humanize-4.0.0 idna-3.3 imageio-2.18.0 importlib-metadata-4.11.3 iniconfig-1.1.1 interface-meta-1.3.0 ivadomed-2.9.5 joblib-1.1.0 kiwisolver-1.4.2 loguru-0.6.0 matplotlib-3.5.1 networkx-2.6.3 nibabel-3.2.2 num2words-0.5.10 numpy-1.18.5 onnxruntime-1.7.0 opt-einsum-3.3.0 packaging-21.3 pandas-1.3.5 pluggy-1.0.0 portalocker-2.4.0 protobuf-3.20.1 psutil-5.9.0 py-1.11.0 pyOpenSSL-22.0.0 pybids-0.15.1 pycparser-2.21 pyparsing-2.4.7 pytest-7.1.2 pytest-console-scripts-1.3.1 pytest-cov-3.0.0 python-dateutil-2.8.2 pytz-2022.1 raven-6.10.0 requests-2.27.1 requirements-parser-0.5.0 scikit-image-0.19.2 scikit-learn-1.0.2 scipy-1.7.3 seaborn-0.11.2 setuptools-62.3.2 six-1.16.0 tensorboard-1.15.0 tensorflow-1.15.5 tensorflow-estimator-1.15.1 termcolor-1.1.0 threadpoolctl-3.1.0 tifffile-2021.11.2 tomli-2.0.1 torch-1.5.0 torchio-0.18.77 torchvision-0.6.0 tqdm-4.64.0 transforms3d-0.3.1 types-setuptools-57.4.14 typing_extensions-4.2.0 urllib3-1.26.9 wheel-0.37.1 wquantiles-0.6 wrapt-1.14.0 xlwt-1.3.0 zipp-3.8.0
+ print info 'Installing spinalcordtoolbox...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling spinalcordtoolbox...\033[0m\n'

Installing spinalcordtoolbox...

+ pip install -e .
Obtaining file:///Users/fmuhamma/sct_5.6
  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-5.6
+ case $OS in
+ sysctl machdep.cpu.brand_string
+ grep -q 'Apple M1'
+ print info 'AVX is supported on this macOS machine. Keeping default TensorFlow...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mAVX is supported on this macOS machine. Keeping default TensorFlow...\033[0m\n'

AVX is supported on this macOS machine. Keeping default TensorFlow...

+ print info 'Creating launchers for Python scripts...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mCreating launchers for Python scripts...\033[0m\n'

Creating launchers for Python scripts...

+ mkdir -p /Users/Fmuhamma/sct_5.6/bin
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/isct_convert_binary_to_trilinear /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/isct_minc2volume-viewer /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/isct_test_ants /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_analyze_lesion /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_analyze_texture /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_apply_transfo /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_check_dependencies /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_compute_ernst_angle /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_compute_hausdorff_distance /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_compute_mscc /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_compute_mtr /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_compute_mtsat /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_compute_snr /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_concat_transfo /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_convert /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_create_mask /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_crop_image /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_deepseg /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_deepseg_gm /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_deepseg_lesion /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_deepseg_sc /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_denoising_onlm /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_detect_pmj /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dice_coefficient /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_compute_bvalue /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_compute_dti /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_concat_b0_and_dwi /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_concat_bvals /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_concat_bvecs /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_denoise_patch2self /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_display_bvecs /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_moco /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_separate_b0_and_dwi /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_dmri_transpose_bvecs /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_download_data /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_extract_metric /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_flatten_sagittal /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_fmri_compute_tsnr /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_fmri_moco /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_get_centerline /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_image /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_label_utils /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_label_vertebrae /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_maths /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_merge_images /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_process_segmentation /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_propseg /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_qc /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_register_multimodal /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_register_to_template /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_resample /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_run_batch /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_smooth_spinalcord /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_straighten_spinalcord /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_testing /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_version /Users/Fmuhamma/sct_5.6/bin/
+ for file in '"$SCT_DIR"/python/envs/venv_sct/bin/*sct*'
+ cp /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/sct_warp_template /Users/Fmuhamma/sct_5.6/bin/
+ export PATH=/Users/Fmuhamma/sct_5.6/bin:/Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin:/Users/Fmuhamma/sct_5.6/python/condabin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
+ PATH=/Users/Fmuhamma/sct_5.6/bin:/Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin:/Users/Fmuhamma/sct_5.6/python/condabin:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
+ [[ -n '' ]]
+ print info 'Installing binaries...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling binaries...\033[0m\n'

Installing binaries...

+ run sct_download_data -d binaries_osx -k
+ print code sct_download_data -d binaries_osx -k
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d binaries_osx -k\033[0m\n'

sct_download_data -d binaries_osx -k

+ sct_download_data -d binaries_osx -k

--
Spinal Cord Toolbox (5.6)

sct_download_data -d binaries_osx -k
--

Trying URL: https://osf.io/874cy?action=download
Downloading: 20200801_sct_binaries_osx.tar.gz

Status:   0%|          | 0.00/60.8M [00:00<?, ?B/s]
Status:  10%|█         | 6.14M/60.8M [00:00<00:01, 51.6MB/s]
Status:  32%|███▏      | 19.2M/60.8M [00:00<00:00, 94.6MB/s]
Status:  53%|█████▎    | 32.0M/60.8M [00:00<00:00, 109MB/s] 
Status:  72%|███████▏  | 43.8M/60.8M [00:00<00:00, 112MB/s]
Status:  91%|█████████▏| 55.5M/60.8M [00:00<00:00, 114MB/s]
Status: 100%|██████████| 60.8M/60.8M [00:00<00:00, 108MB/s]Creating temporary folder (/var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114830.664936-iq0racpd)
Unzip data to: /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114830.664936-iq0racpd
Copying data to: /Users/fmuhamma/sct_5.6/bin
Removing temporary folders...

Done!

+ print info 'All requirements installed!'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mAll requirements installed!\033[0m\n'

All requirements installed!

+ [[ -n '' ]]
+ print info 'Installing data...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mInstalling data...\033[0m\n'

Installing data...

+ run rm -rf /Users/Fmuhamma/sct_5.6/data
+ print code rm -rf /Users/Fmuhamma/sct_5.6/data
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mrm -rf /Users/Fmuhamma/sct_5.6/data\033[0m\n'

rm -rf /Users/Fmuhamma/sct_5.6/data

+ rm -rf /Users/Fmuhamma/sct_5.6/data
+ run mkdir -p /Users/Fmuhamma/sct_5.6/data
+ print code mkdir -p /Users/Fmuhamma/sct_5.6/data
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34mmkdir -p /Users/Fmuhamma/sct_5.6/data\033[0m\n'

mkdir -p /Users/Fmuhamma/sct_5.6/data

+ mkdir -p /Users/Fmuhamma/sct_5.6/data
+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d PAM50
+ print code sct_download_data -d PAM50
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d PAM50\033[0m\n'

sct_download_data -d PAM50

+ sct_download_data -d PAM50

--
Spinal Cord Toolbox (5.6)

sct_download_data -d PAM50
--

Trying URL: https://github.com/spinalcordtoolbox/PAM50/releases/download/r20201104/PAM50-r20201104.zip
Downloading: PAM50-r20201104.zip

Status:   0%|          | 0.00/70.9M [00:00<?, ?B/s]
Status:   0%|          | 131k/70.9M [00:00<01:03, 1.12MB/s]
Status:   1%|▏         | 918k/70.9M [00:00<00:16, 4.16MB/s]
Status:   5%|▌         | 3.67M/70.9M [00:00<00:05, 12.2MB/s]
Status:  10%|▉         | 6.79M/70.9M [00:00<00:03, 18.6MB/s]
Status:  18%|█▊        | 12.6M/70.9M [00:00<00:01, 30.6MB/s]
Status:  24%|██▎       | 16.8M/70.9M [00:00<00:02, 22.7MB/s]
Status:  30%|██▉       | 21.0M/70.9M [00:00<00:01, 27.0MB/s]
Status:  36%|███▌      | 25.6M/70.9M [00:01<00:01, 31.7MB/s]
Status:  47%|████▋     | 33.6M/70.9M [00:01<00:00, 42.6MB/s]
Status:  59%|█████▉    | 42.0M/70.9M [00:01<00:00, 51.8MB/s]
Status:  71%|███████   | 50.3M/70.9M [00:01<00:00, 58.7MB/s]
Status:  80%|███████▉  | 56.5M/70.9M [00:01<00:00, 58.0MB/s]
Status:  91%|█████████ | 64.3M/70.9M [00:01<00:00, 63.5MB/s]
Status: 100%|██████████| 70.9M/70.9M [00:01<00:00, 42.5MB/s]Creating temporary folder (/var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114834.739127-x6b8ibu2)
Unzip data to: /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114834.739127-x6b8ibu2
Copying data to: /Users/fmuhamma/sct_5.6/data/PAM50
Removing temporary folders...

Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d gm_model
+ print code sct_download_data -d gm_model
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d gm_model\033[0m\n'

sct_download_data -d gm_model

+ sct_download_data -d gm_model

--
Spinal Cord Toolbox (5.6)

sct_download_data -d gm_model
--

Trying URL: https://osf.io/ugscu/?action=download
Downloading: 20160922_gm_model.zip

Status:   0%|          | 0.00/10.3M [00:00<?, ?B/s]
Status:  47%|████▋     | 4.85M/10.3M [00:00<00:00, 48.4MB/s]
Status: 100%|██████████| 10.3M/10.3M [00:00<00:00, 65.4MB/s]Creating temporary folder (/var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114836.604429-_azfnxsd)
Unzip data to: /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114836.604429-_azfnxsd
Copying data to: /Users/fmuhamma/sct_5.6/data/gm_model
Removing temporary folders...

Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d optic_models
+ print code sct_download_data -d optic_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d optic_models\033[0m\n'

sct_download_data -d optic_models

+ sct_download_data -d optic_models

--
Spinal Cord Toolbox (5.6)

sct_download_data -d optic_models
--

Trying URL: https://github.com/spinalcordtoolbox/optic_models/releases/download/r20170413/20170413_optic_models.zip
Downloading: 20170413_optic_models.zip

Status:   0%|          | 0.00/17.7k [00:00<?, ?B/s]
Status: 100%|██████████| 17.7k/17.7k [00:00<00:00, 61.1MB/s]Creating temporary folder (/var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114837.725723-yz459rjt)
Unzip data to: /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114837.725723-yz459rjt
Copying data to: /Users/fmuhamma/sct_5.6/data/optic_models
Removing temporary folders...

Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d pmj_models
+ print code sct_download_data -d pmj_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d pmj_models\033[0m\n'

sct_download_data -d pmj_models

+ sct_download_data -d pmj_models

--
Spinal Cord Toolbox (5.6)

sct_download_data -d pmj_models
--

Trying URL: https://github.com/spinalcordtoolbox/pmj_models/releases/download/r20170922/20170922_pmj_models.zip
Downloading: 20170922_pmj_models.zip

Status:   0%|          | 0.00/8.87k [00:00<?, ?B/s]
Status: 100%|██████████| 8.87k/8.87k [00:00<00:00, 43.9MB/s]Creating temporary folder (/var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114838.608377-pukr7v9_)
Unzip data to: /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114838.608377-pukr7v9_
Copying data to: /Users/fmuhamma/sct_5.6/data/pmj_models
Removing temporary folders...

Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d deepseg_sc_models
+ print code sct_download_data -d deepseg_sc_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d deepseg_sc_models\033[0m\n'

sct_download_data -d deepseg_sc_models

+ sct_download_data -d deepseg_sc_models

--
Spinal Cord Toolbox (5.6)

sct_download_data -d deepseg_sc_models
--

Trying URL: https://github.com/spinalcordtoolbox/deepseg_sc_models/releases/download/r20180610/20180610_deepseg_sc_models.zip
Downloading: 20180610_deepseg_sc_models.zip

Status:   0%|          | 0.00/58.7M [00:00<?, ?B/s]
Status:  14%|█▍        | 8.44M/58.7M [00:00<00:00, 84.4MB/s]
Status:  29%|██▊       | 16.9M/58.7M [00:00<00:00, 75.0MB/s]
Status:  42%|████▏     | 24.5M/58.7M [00:00<00:00, 66.0MB/s]
Status:  53%|█████▎    | 31.2M/58.7M [00:00<00:00, 64.9MB/s]
Status:  64%|██████▍   | 37.8M/58.7M [00:00<00:00, 63.3MB/s]
Status:  75%|███████▌  | 44.1M/58.7M [00:00<00:00, 59.2MB/s]
Status:  86%|████████▌ | 50.3M/58.7M [00:00<00:00, 59.5MB/s]
Status:  97%|█████████▋| 57.1M/58.7M [00:00<00:00, 61.2MB/s]
Status: 100%|██████████| 58.7M/58.7M [00:00<00:00, 63.9MB/s]Creating temporary folder (/var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114840.376193-htwts2e6)
Unzip data to: /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114840.376193-htwts2e6
Copying data to: /Users/fmuhamma/sct_5.6/data/deepseg_sc_models
Removing temporary folders...

Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d deepseg_gm_models
+ print code sct_download_data -d deepseg_gm_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d deepseg_gm_models\033[0m\n'

sct_download_data -d deepseg_gm_models

+ sct_download_data -d deepseg_gm_models

--
Spinal Cord Toolbox (5.6)

sct_download_data -d deepseg_gm_models
--

Trying URL: https://github.com/spinalcordtoolbox/deepseg_gm_models/releases/download/r20180205/20180205_deepseg_gm_models.zip
Downloading: 20180205_deepseg_gm_models.zip

Status:   0%|          | 0.00/2.28M [00:00<?, ?B/s]
Status: 100%|██████████| 2.28M/2.28M [00:00<00:00, 50.1MB/s]Creating temporary folder (/var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114841.664229-nlb0sprb)
Unzip data to: /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114841.664229-nlb0sprb
Copying data to: /Users/fmuhamma/sct_5.6/data/deepseg_gm_models
Removing temporary folders...

Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d deepseg_lesion_models
+ print code sct_download_data -d deepseg_lesion_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d deepseg_lesion_models\033[0m\n'

sct_download_data -d deepseg_lesion_models

+ sct_download_data -d deepseg_lesion_models

--
Spinal Cord Toolbox (5.6)

sct_download_data -d deepseg_lesion_models
--

Trying URL: https://github.com/spinalcordtoolbox/deepseg_lesion_models/releases/download/r20180613/20180613_deepseg_lesion_models.zip
Downloading: 20180613_deepseg_lesion_models.zip

Status:   0%|          | 0.00/16.0M [00:00<?, ?B/s]
Status:   1%|          | 115k/16.0M [00:00<00:15, 1.05MB/s]
Status:   4%|▍         | 623k/16.0M [00:00<00:05, 2.86MB/s]
Status:  16%|█▌        | 2.51M/16.0M [00:00<00:01, 8.42MB/s]
Status:  28%|██▊       | 4.54M/16.0M [00:00<00:00, 12.5MB/s]
Status:  56%|█████▌    | 8.90M/16.0M [00:00<00:00, 22.7MB/s]
Status:  89%|████████▉ | 14.3M/16.0M [00:00<00:00, 32.7MB/s]
Status: 100%|██████████| 16.0M/16.0M [00:00<00:00, 21.6MB/s]Creating temporary folder (/var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114843.399957-mn7qkgyx)
Unzip data to: /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114843.399957-mn7qkgyx
Copying data to: /Users/fmuhamma/sct_5.6/data/deepseg_lesion_models
Removing temporary folders...

Done!

+ for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models
+ run sct_download_data -d c2c3_disc_models
+ print code sct_download_data -d c2c3_disc_models
+ type=code
+ shift
+ case "$type" in
+ echo -e '\n\033[0;34msct_download_data -d c2c3_disc_models\033[0m\n'

sct_download_data -d c2c3_disc_models

+ sct_download_data -d c2c3_disc_models

--
Spinal Cord Toolbox (5.6)

sct_download_data -d c2c3_disc_models
--

Trying URL: https://github.com/spinalcordtoolbox/c2c3_disc_models/releases/download/r20190117/20190117_c2c3_disc_models.zip
Downloading: 20190117_c2c3_disc_models.zip

Status:   0%|          | 0.00/8.94k [00:00<?, ?B/s]
Status: 100%|██████████| 8.94k/8.94k [00:00<00:00, 40.2MB/s]Creating temporary folder (/var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114844.325863-mzbmbtmg)
Unzip data to: /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/sct-20220522114844.325863-mzbmbtmg
Copying data to: /Users/fmuhamma/sct_5.6/data/c2c3_disc_models
Removing temporary folders...

Done!

+ python -c 'import spinalcordtoolbox.deepseg.models; spinalcordtoolbox.deepseg.models.install_default_models()'

Status:   0%|          | 0.00/18.0M [00:00<?, ?B/s]
Status:   3%|▎         | 606k/18.0M [00:00<00:03, 4.78MB/s]
Status:  12%|█▏        | 2.09M/18.0M [00:00<00:01, 10.1MB/s]
Status:  23%|██▎       | 4.20M/18.0M [00:00<00:01, 12.5MB/s]
Status:  47%|████▋     | 8.40M/18.0M [00:00<00:00, 22.0MB/s]
Status:  70%|██████▉   | 12.6M/18.0M [00:00<00:00, 28.4MB/s]
Status: 100%|██████████| 18.0M/18.0M [00:00<00:00, 28.0MB/s]
+ conda deactivate
+ [[ -e /Users/Fmuhamma/.bashrc ]]
+ [[ y =~ ^[Yy] ]]
+ edit_shellrc
+ echo
+ echo ''
++ date '+%Y-%m-%d %H:%M:%S'
+ echo '# SPINALCORDTOOLBOX (installed on 2022-05-22 11:48:46)'
+ echo 'export PATH="/Users/Fmuhamma/sct_5.6/bin:$PATH"'
+ [[ bash == \b\a\s\h ]]
+ echo 'export SCT_DIR=/Users/Fmuhamma/sct_5.6'
+ echo ''
+ [[ -n '' ]]
+ print info 'Validate installation...'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mValidate installation...\033[0m\n'

Validate installation...

+ sct_check_dependencies

--
Spinal Cord Toolbox (5.6)

sct_check_dependencies 
--

SCT info:
- version: 5.6
- path: /Users/fmuhamma/sct_5.6
OS: osx (Darwin-20.6.0-x86_64-i386-64bit)
CPU cores: Available: 16, Used by ITK functions: 16
RAM: Total: 65536MB, Used: 22938MB, Available: 42593MB
Check Python executable.............................[WARNING]
  Using system python which is unsupported: /Users/Fmuhamma/sct_5.6/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if dipy is installed..........................[OK] (1.5.0)
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras (2.3.1) is installed.................[OK] (2.3.1)
Check if ivadomed is installed......................[OK] (2.9.5)
Check if matplotlib is installed....................[OK] (3.5.1)
Check if nibabel is installed.......................[OK] (3.2.2)
Check if numpy is installed.........................[OK] (1.18.5)
Check if onnxruntime is installed...................[OK] (1.7.0)
Check if pandas is installed........................[OK] (1.3.5)
Check if portalocker is installed...................[OK] (2.4.0)
Check if psutil is installed........................[OK] (5.9.0)
Check if pyqt5 (5.11.3) is installed................[OK] (5.11.3)
Check if pytest is installed........................[OK] (7.1.2)
Check if pytest-cov is installed....................[OK] (3.0.0)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.27.1)
Check if requirements-parser is installed...........[OK]
Check if scipy is installed.........................[OK] (1.7.3)
Check if scikit-image is installed..................[OK] (0.19.2)
Check if scikit-learn is installed..................[OK] (1.0.2)
Check if tensorflow is installed....................[OK] (1.15.5)
Check if torch (1.5.0) is installed.................[OK] (1.5.0)
Check if torchvision (0.6.0) is installed...........[OK] (0.6.0)
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.64.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3 is installed.......................[OK] (1.26.9)
Check if pytest_console_scripts is installed........[OK]
Check if wquantiles is installed....................[OK] (0.4)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
[OK]
Check if figure can be opened with matplotlib.......[OK] (Using GUI backend: 'MacOSX')
Check if figure can be opened with PyQt.............[OK]
Check FSLeyes version...............................[OK] (1.3.0)

+ [[ y =~ ^[Nn] ]]
+ print info 'Open a new Terminal window to load environment variables, or run:
  source /Users/Fmuhamma/.bashrc'
+ type=info
+ shift
+ case "$type" in
+ echo -e '\n\033[0;32mOpen a new Terminal window to load environment variables, or run:
  source /Users/Fmuhamma/.bashrc\033[0m\n'

Open a new Terminal window to load environment variables, or run:
  source /Users/Fmuhamma/.bashrc

++ finish
++ value=0
++ [[ 0 -eq 0 ]]
++ print info 'Installation finished successfully!'
++ type=info
++ shift
++ case "$type" in
++ echo -e '\n\033[0;32mInstallation finished successfully!\033[0m\n'

Installation finished successfully!

++ rm -rf /var/folders/nk/wc5k121s0ddfyld7z4jmqddh0000gq/T/tmp.HwlGnP63
++ exit 0