[NEURODOCKER 2021-06-24 23:25:56,365 INFO]: running command within container f7a075905ebd5bc4ed978d07ade02e0463bf21c2edf91179dcb47ae3aa5ba054: bash /tmp/_trace.sh "mri_convert /home/T1.nii.gz /home/T1.mgz" "mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2"
[NEURODOCKER 2021-06-24 23:25:56,492 INFO]: NEURODOCKER (in container): installing dedicated Miniconda and ReproZip.
[NEURODOCKER 2021-06-24 23:25:56,492 INFO]: + REPROZIP_CONDA=/tmp/reprozip-miniconda
+ REPROZIP_TRACE_DIR=/tmp/neurodocker-reprozip-trace
+ CONDA_URL=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ NEURODOCKER_LOG_PREFIX='NEURODOCKER (in container)'
+ '[' 2 -eq 0 ']'
+ '[' -d /tmp/neurodocker-reprozip-trace ']'
+ program_exists bzip2
+ hash bzip2
+ program_exists curl
+ hash curl
+ '[' '!' -f /tmp/reprozip-miniconda/bin/reprozip ']'
+ echo 'NEURODOCKER (in container): installing dedicated Miniconda and ReproZip.'
+ install_conda_reprozip
+ TMP_CONDA_INSTALLER=/tmp/miniconda.sh
+ ls /tmp
[NEURODOCKER 2021-06-24 23:25:56,502 INFO]: _trace.sh
[NEURODOCKER 2021-06-24 23:25:56,503 INFO]: + curl -sSL -o /tmp/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
[NEURODOCKER 2021-06-24 23:26:05,292 INFO]: + ls /tmp
[NEURODOCKER 2021-06-24 23:26:05,295 INFO]: miniconda.sh
_trace.sh
[NEURODOCKER 2021-06-24 23:26:05,298 INFO]: + bash /tmp/miniconda.sh -b -f -p /tmp/reprozip-miniconda
[NEURODOCKER 2021-06-24 23:26:05,325 INFO]: PREFIX=/tmp/reprozip-miniconda
[NEURODOCKER 2021-06-24 23:26:05,941 INFO]: Unpacking payload ...
[NEURODOCKER 2021-06-24 23:26:27,484 INFO]: 0%|          | 0/36 [00:00<?, ?it/s]
[NEURODOCKER 2021-06-24 23:26:28,883 INFO]: Extracting : conda-4.9.2-py38h06a4308_0.conda:   0%|          | 0/36 [00:01<?, ?it/s]
Extracting : conda-4.9.2-py38h06a4308_0.conda:   3%|▎         | 1/36 [00:01<00:49,  1.40s/it]
[NEURODOCKER 2021-06-24 23:26:28,895 INFO]: Extracting : urllib3-1.25.11-py_0.conda:   3%|▎         | 1/36 [00:01<00:49,  1.40s/it]      
Extracting : tqdm-4.51.0-pyhd3eb1b0_0.conda:   6%|▌         | 2/36 [00:01<00:47,  1.40s/it]
[NEURODOCKER 2021-06-24 23:26:28,919 INFO]: Extracting : openssl-1.1.1h-h7b6447c_0.conda:   8%|▊         | 3/36 [00:01<00:46,  1.40s/it]
Extracting : requests-2.24.0-py_0.conda:  11%|█         | 4/36 [00:01<00:44,  1.40s/it]     
Extracting : certifi-2020.6.20-pyhd3eb1b0_3.conda:  14%|█▍        | 5/36 [00:01<00:43,  1.40s/it]
Extracting : pysocks-1.7.1-py38h06a4308_0.conda:  17%|█▋        | 6/36 [00:01<00:42,  1.40s/it]  
Extracting : cffi-1.14.3-py38h261ae71_2.conda:  19%|█▉        | 7/36 [00:01<00:40,  1.40s/it]  
Extracting : ld_impl_linux-64-2.33.1-h53a641e_7.conda:  22%|██▏       | 8/36 [00:01<00:39,  1.40s/it]
Extracting : ca-certificates-2020.10.14-0.conda:  25%|██▌       | 9/36 [00:01<00:37,  1.40s/it]      
Extracting : yaml-0.2.5-h7b6447c_0.conda:  28%|██▊       | 10/36 [00:01<00:36,  1.40s/it]
[NEURODOCKER 2021-06-24 23:26:32,974 INFO]: Extracting : python-3.8.5-h7579374_1.conda:  31%|███       | 11/36 [00:05<00:35,  1.40s/it]
Extracting : python-3.8.5-h7579374_1.conda:  33%|███▎      | 12/36 [00:05<00:26,  1.09s/it]
Extracting : libffi-3.3-he6710b0_2.conda:  33%|███▎      | 12/36 [00:05<00:26,  1.09s/it]  
Extracting : libedit-3.1.20191231-h14c3975_1.conda:  36%|███▌      | 13/36 [00:05<00:25,  1.09s/it]
Extracting : six-1.15.0-py38h06a4308_0.conda:  39%|███▉      | 14/36 [00:05<00:24,  1.09s/it]      
Extracting : xz-5.2.5-h7b6447c_0.conda:  42%|████▏     | 15/36 [00:05<00:22,  1.09s/it]      
Extracting : ncurses-6.2-he6710b0_1.conda:  44%|████▍     | 16/36 [00:05<00:21,  1.09s/it]
Extracting : pip-20.2.4-py38h06a4308_0.conda:  47%|████▋     | 17/36 [00:05<00:20,  1.09s/it]
Extracting : libgcc-ng-9.1.0-hdf63c60_0.conda:  50%|█████     | 18/36 [00:05<00:19,  1.09s/it]
Extracting : setuptools-50.3.1-py38h06a4308_1.conda:  53%|█████▎    | 19/36 [00:05<00:18,  1.09s/it]
Extracting : pyopenssl-19.1.0-pyhd3eb1b0_1.conda:  56%|█████▌    | 20/36 [00:05<00:17,  1.09s/it]   
Extracting : brotlipy-0.7.0-py38h27cfd23_1003.conda:  58%|█████▊    | 21/36 [00:05<00:16,  1.09s/it]
Extracting : readline-8.0-h7b6447c_0.conda:  61%|██████    | 22/36 [00:05<00:15,  1.09s/it]         
Extracting : chardet-3.0.4-py38h06a4308_1003.conda:  64%|██████▍   | 23/36 [00:05<00:14,  1.09s/it]
Extracting : _libgcc_mutex-0.1-main.conda:  67%|██████▋   | 24/36 [00:05<00:13,  1.09s/it]         
Extracting : cryptography-3.2.1-py38h3c74f83_1.conda:  69%|██████▉   | 25/36 [00:05<00:12,  1.09s/it]
Extracting : ruamel_yaml-0.15.87-py38h7b6447c_1.conda:  72%|███████▏  | 26/36 [00:05<00:10,  1.09s/it]
Extracting : pycparser-2.20-py_2.conda:  75%|███████▌  | 27/36 [00:05<00:09,  1.09s/it]
[NEURODOCKER 2021-06-24 23:26:32,975 INFO]: Extracting : wheel-0.35.1-pyhd3eb1b0_0.conda:  78%|███████▊  | 28/36 [00:05<00:08,  1.09s/it]
Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda:  81%|████████  | 29/36 [00:05<00:07,  1.09s/it]
Extracting : conda-package-handling-1.7.2-py38h03888b9_0.conda:  83%|████████▎ | 30/36 [00:05<00:06,  1.09s/it]
[NEURODOCKER 2021-06-24 23:26:32,975 INFO]: Extracting : pycosat-0.6.3-py38h7b6447c_1.conda:  86%|████████▌ | 31/36 [00:05<00:05,  1.09s/it]               
Extracting : zlib-1.2.11-h7b6447c_3.conda:  89%|████████▉ | 32/36 [00:05<00:04,  1.09s/it]      
Extracting : idna-2.10-py_0.conda:  92%|█████████▏| 33/36 [00:05<00:03,  1.09s/it]
[NEURODOCKER 2021-06-24 23:26:32,976 INFO]: Extracting : tk-8.6.10-hbc83047_0.conda:  94%|█████████▍| 34/36 [00:05<00:02,  1.09s/it]
[NEURODOCKER 2021-06-24 23:26:32,977 INFO]: Extracting : sqlite-3.33.0-h62c20be_0.conda:  97%|█████████▋| 35/36 [00:05<00:01,  1.09s/it]
[NEURODOCKER 2021-06-24 23:26:32,984 INFO]: 
[NEURODOCKER 2021-06-24 23:26:33,101 INFO]: 
[NEURODOCKER 2021-06-24 23:26:36,136 INFO]: Collecting package metadata (current_repodata.json):
[NEURODOCKER 2021-06-24 23:26:36,137 INFO]: ...working...
[NEURODOCKER 2021-06-24 23:26:36,193 INFO]: done
[NEURODOCKER 2021-06-24 23:26:36,193 INFO]: Solving environment:
[NEURODOCKER 2021-06-24 23:26:36,193 INFO]: ...working...
[NEURODOCKER 2021-06-24 23:26:36,573 INFO]: done
[NEURODOCKER 2021-06-24 23:26:36,610 INFO]: ## Package Plan ##

  environment location: /tmp/reprozip-miniconda

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - brotlipy==0.7.0=py38h27cfd23_1003
    - ca-certificates==2020.10.14=0
    - certifi==2020.6.20=pyhd3eb1b0_3
    - cffi==1.14.3=py38h261ae71_2
    - chardet==3.0.4=py38h06a4308_1003
    - conda-package-handling==1.7.2=py38h03888b9_0
    - conda==4.9.2=py38h06a4308_0
    - cryptography==3.2.1=py38h3c74f83_1
    - idna==2.10=py_0
    - ld_impl_linux-64==2.33.1=h53a641e_7
    - libedit==3.1.20191231=h14c3975_1
    - libffi==3.3=he6710b0_2
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.2=he6710b0_1
    - openssl==1.1.1h=h7b6447c_0
    - pip==20.2.4=py38h06a4308_0
    - pycosat==0.6.3=py38h7b6447c_1
    - pycparser==2.20=py_2
    - pyopenssl==19.1.0=pyhd3eb1b0_1
    - pysocks==1.7.1=py38h06a4308_0
    - python==3.8.5=h7579374_1
    - readline==8.0=h7b6447c_0
    - requests==2.24.0=py_0
    - ruamel_yaml==0.15.87=py38h7b6447c_1
    - setuptools==50.3.1=py38h06a4308_1
    - six==1.15.0=py38h06a4308_0
    - sqlite==3.33.0=h62c20be_0
    - tk==8.6.10=hbc83047_0
    - tqdm==4.51.0=pyhd3eb1b0_0
    - urllib3==1.25.11=py_0
    - wheel==0.35.1=pyhd3eb1b0_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.2.5=h7b6447c_0
    - zlib==1.2.11=h7b6447c_3


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  brotlipy           pkgs/main/linux-64::brotlipy-0.7.0-py38h27cfd23_1003
  ca-certificates    pkgs/main/linux-64::ca-certificates-2020.10.14-0
  certifi            pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
  cffi               pkgs/main/linux-64::cffi-1.14.3-py38h261ae71_2
  chardet            pkgs/main/linux-64::chardet-3.0.4-py38h06a4308_1003
  conda              pkgs/main/linux-64::conda-4.9.2-py38h06a4308_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.7.2-py38h03888b9_0
  cryptography       pkgs/main/linux-64::cryptography-3.2.1-py38h3c74f83_1
  idna               pkgs/main/noarch::idna-2.10-py_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libedit            pkgs/main/linux-64::libedit-3.1.20191231-h14c3975_1
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1h-h7b6447c_0
  pip                pkgs/main/linux-64::pip-20.2.4-py38h06a4308_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py38h7b6447c_1
  pycparser          pkgs/main/noarch::pycparser-2.20-py_2
  pyopenssl          pkgs/main/noarch::pyopenssl-19.1.0-pyhd3eb1b0_1
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py38h06a4308_0
  python             pkgs/main/linux-64::python-3.8.5-h7579374_1
  readline           pkgs/main/linux-64::readline-8.0-h7b6447c_0
  requests           pkgs/main/noarch::requests-2.24.0-py_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.87-py38h7b6447c_1
  setuptools         pkgs/main/linux-64::setuptools-50.3.1-py38h06a4308_1
  six                pkgs/main/linux-64::six-1.15.0-py38h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0
  tk                 pkgs/main/linux-64::tk-8.6.10-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.51.0-pyhd3eb1b0_0
  urllib3            pkgs/main/noarch::urllib3-1.25.11-py_0
  wheel              pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Preparing transaction: ...working...
[NEURODOCKER 2021-06-24 23:26:37,265 INFO]: done
[NEURODOCKER 2021-06-24 23:26:37,266 INFO]: Executing transaction:
[NEURODOCKER 2021-06-24 23:26:37,266 INFO]: ...working...
[NEURODOCKER 2021-06-24 23:26:39,301 INFO]: done
[NEURODOCKER 2021-06-24 23:26:40,070 INFO]: installation finished.
[NEURODOCKER 2021-06-24 23:26:40,072 INFO]: + rm -f /tmp/miniconda.sh
[NEURODOCKER 2021-06-24 23:26:40,152 INFO]: + /tmp/reprozip-miniconda/bin/python -m pip install --no-cache-dir reprozip
[NEURODOCKER 2021-06-24 23:26:40,756 INFO]: Collecting reprozip
[NEURODOCKER 2021-06-24 23:26:40,800 INFO]: Downloading reprozip-1.0.16-cp38-cp38-manylinux2010_x86_64.whl (749 kB)
[NEURODOCKER 2021-06-24 23:26:40,943 INFO]: Collecting distro
[NEURODOCKER 2021-06-24 23:26:40,950 INFO]: Downloading distro-1.5.0-py2.py3-none-any.whl (18 kB)
[NEURODOCKER 2021-06-24 23:26:40,996 INFO]: Collecting rpaths>=0.8
[NEURODOCKER 2021-06-24 23:26:41,004 INFO]: Downloading rpaths-0.13-py2.py3-none-any.whl (12 kB)
[NEURODOCKER 2021-06-24 23:26:41,057 INFO]: Collecting usagestats>=0.3
[NEURODOCKER 2021-06-24 23:26:41,067 INFO]: Downloading usagestats-1.0-py2.py3-none-any.whl (10 kB)
[NEURODOCKER 2021-06-24 23:26:41,228 INFO]: Collecting PyYAML
[NEURODOCKER 2021-06-24 23:26:41,238 INFO]: Downloading PyYAML-5.4.1-cp38-cp38-manylinux1_x86_64.whl (662 kB)
[NEURODOCKER 2021-06-24 23:26:41,296 INFO]: Requirement already satisfied: requests in /tmp/reprozip-miniconda/lib/python3.8/site-packages (from reprozip) (2.24.0)
[NEURODOCKER 2021-06-24 23:26:41,315 INFO]: Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /tmp/reprozip-miniconda/lib/python3.8/site-packages (from requests->reprozip) (1.25.11)
[NEURODOCKER 2021-06-24 23:26:41,337 INFO]: Requirement already satisfied: certifi>=2017.4.17 in /tmp/reprozip-miniconda/lib/python3.8/site-packages (from requests->reprozip) (2020.6.20)
[NEURODOCKER 2021-06-24 23:26:41,338 INFO]: Requirement already satisfied: chardet<4,>=3.0.2 in /tmp/reprozip-miniconda/lib/python3.8/site-packages (from requests->reprozip) (3.0.4)
[NEURODOCKER 2021-06-24 23:26:41,340 INFO]: Requirement already satisfied: idna<3,>=2.5 in /tmp/reprozip-miniconda/lib/python3.8/site-packages (from requests->reprozip) (2.10)
[NEURODOCKER 2021-06-24 23:26:41,460 INFO]: Installing collected packages: distro, rpaths, usagestats, PyYAML, reprozip
[NEURODOCKER 2021-06-24 23:26:41,698 INFO]: Successfully installed PyYAML-5.4.1 distro-1.5.0 reprozip-1.0.16 rpaths-0.13 usagestats-1.0
[NEURODOCKER 2021-06-24 23:26:41,981 INFO]: + echo 'NEURODOCKER (in container): running reprozip trace command(s)'
+ run_reprozip_trace 'mri_convert /home/T1.nii.gz /home/T1.mgz' 'mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2'
+ cmds=("$@")
[NEURODOCKER 2021-06-24 23:26:41,981 INFO]: NEURODOCKER (in container): running reprozip trace command(s)
[NEURODOCKER 2021-06-24 23:26:41,981 INFO]: + reprozip_base_cmd='/tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages'
+ for cmd in '"${cmds[@]}"'
+ '[' 'mri_convert /home/T1.nii.gz /home/T1.mgz' == 'mri_convert /home/T1.nii.gz /home/T1.mgz' ']'
+ continue_=--overwrite
+ reprozip_cmd='/tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --overwrite mri_convert /home/T1.nii.gz /home/T1.mgz'
+ printf 'NEURODOCKER (in container): executing command: /tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --overwrite mri_convert /home/T1.nii.gz /home/T1.mgz\n'
+ /tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --overwrite mri_convert /home/T1.nii.gz /home/T1.mgz
[NEURODOCKER 2021-06-24 23:26:41,982 INFO]: NEURODOCKER (in container): executing command: /tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --overwrite mri_convert /home/T1.nii.gz /home/T1.mgz
[NEURODOCKER 2021-06-24 23:26:42,475 INFO]: mri_convert /home/T1.nii.gz /home/T1.mgz
[NEURODOCKER 2021-06-24 23:26:55,364 INFO]: reading from /home/T1.nii.gz...
TR=7.17, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.996184, 0.0748968, -0.0448036)
j_ras = (-0.074953, 0.997187, 0.000427244)
k_ras = (0.0447098, 0.00292976, 0.998996)
writing to /home/T1.mgz...
[NEURODOCKER 2021-06-24 23:26:55,563 INFO]: [REPROZIP] 13:26:55.569 WARNING: Some files were read and then written. We will only pack the final version of the file; reproducible experiments shouldn't change their input files
[NEURODOCKER 2021-06-24 23:26:55,590 INFO]: Uploading usage statistics is currently disabled
Please help us by providing anonymous usage statistics; you can enable this
by running:
    reprozip usage_report --enable
If you do not want to see this message again, you can run:
    reprozip usage_report --disable
Nothing will be uploaded before you opt in.
[NEURODOCKER 2021-06-24 23:26:55,590 INFO]: Configuration file written in /tmp/neurodocker-reprozip-trace/config.yml
Edit that file then run the packer -- use 'reprozip pack -h' for help
[NEURODOCKER 2021-06-24 23:26:55,646 INFO]: NEURODOCKER (in container): executing command: /tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --continue mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2
[NEURODOCKER 2021-06-24 23:26:55,646 INFO]: + for cmd in '"${cmds[@]}"'
+ '[' 'mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2' == 'mri_convert /home/T1.nii.gz /home/T1.mgz' ']'
+ continue_=--continue
+ reprozip_cmd='/tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --continue mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2'
+ printf 'NEURODOCKER (in container): executing command: /tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --continue mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2\n'
+ /tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --continue mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2
[NEURODOCKER 2021-06-24 23:26:56,295 INFO]: /usr/bin/bc
[NEURODOCKER 2021-06-24 23:26:56,550 INFO]: /
[NEURODOCKER 2021-06-24 23:26:56,594 INFO]: /opt/freesurfer-7.1.1/bin/mri_nu_correct.mni
[NEURODOCKER 2021-06-24 23:26:56,621 INFO]: --i /home/T1.mgz --o /home/T1_N3.mgz --n 2
[NEURODOCKER 2021-06-24 23:26:56,674 INFO]: nIters 2
[NEURODOCKER 2021-06-24 23:26:56,732 INFO]: mri_nu_correct.mni 7.1.1
[NEURODOCKER 2021-06-24 23:26:56,782 INFO]: Linux f7a075905ebd 5.10.25-linuxkit #1 SMP Tue Mar 23 09:27:39 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
[NEURODOCKER 2021-06-24 23:26:56,843 INFO]: Thu Jun 24 13:26:56 UTC 2021
[NEURODOCKER 2021-06-24 23:26:57,065 INFO]: tmpdir is /home/tmp.mri_nu_correct.mni.114
[NEURODOCKER 2021-06-24 23:26:57,091 INFO]: nu_correct: Command not found.
[NEURODOCKER 2021-06-24 23:26:57,184 INFO]: /
[NEURODOCKER 2021-06-24 23:26:57,214 INFO]: mri_convert /home/T1.mgz /home/tmp.mri_nu_correct.mni.114/nu0.mnc -odt float
[NEURODOCKER 2021-06-24 23:26:57,363 INFO]: mri_convert /home/T1.mgz /home/tmp.mri_nu_correct.mni.114/nu0.mnc -odt float
[NEURODOCKER 2021-06-24 23:27:37,296 INFO]: reading from /home/T1.mgz...
TR=7.17, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.996184, 0.0748968, -0.0448036)
j_ras = (-0.074953, 0.997187, 0.000427244)
k_ras = (0.0447098, 0.00292976, 0.998996)
changing data type from short to float (noscale = 0)...
writing to /home/tmp.mri_nu_correct.mni.114/nu0.mnc...
Outputting Volume: ........
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[NEURODOCKER 2021-06-24 23:28:17,390 INFO]: --------------------------------------------------------
[NEURODOCKER 2021-06-24 23:28:17,585 INFO]: Iteration 1 Thu Jun 24 13:28:17 UTC 2021
[NEURODOCKER 2021-06-24 23:28:17,671 INFO]: nu_correct -clobber /home/tmp.mri_nu_correct.mni.114/nu0.mnc /home/tmp.mri_nu_correct.mni.114/nu1.mnc -tmpdir /home/tmp.mri_nu_correct.mni.114/0/
[NEURODOCKER 2021-06-24 23:28:17,862 INFO]: nu_correct: Command not found.
[NEURODOCKER 2021-06-24 23:28:17,891 INFO]: ERROR: nu_correct
[NEURODOCKER 2021-06-24 23:28:17,911 INFO]: [REPROZIP] 13:28:17.918 WARNING: Program exited with non-zero code 1
[NEURODOCKER 2021-06-24 23:28:18,433 INFO]: [REPROZIP] 13:28:18.440 WARNING: Some files were read and then written. We will only pack the final version of the file; reproducible experiments shouldn't change their input files
[NEURODOCKER 2021-06-24 23:28:18,565 INFO]: Uploading usage statistics is currently disabled
Please help us by providing anonymous usage statistics; you can enable this
by running:
    reprozip usage_report --enable
If you do not want to see this message again, you can run:
    reprozip usage_report --disable
Nothing will be uploaded before you opt in.
[NEURODOCKER 2021-06-24 23:28:18,565 INFO]: Configuration file written in /tmp/neurodocker-reprozip-trace/config.yml
Edit that file then run the packer -- use 'reprozip pack -h' for help
[NEURODOCKER 2021-06-24 23:28:18,675 INFO]: NEURODOCKER (in container): ERROR: reprozip trace command exited with non-zero code. Command: /tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --continue mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2
Traceback (most recent call last):
  File "/opt/miniconda3/envs/neurodocker/bin/neurodocker-minify", line 8, in <module>
    sys.exit(main())
  File "/opt/miniconda3/envs/neurodocker/lib/python3.9/site-packages/neurodocker/reprozip/gentle/trace.py", line 169, in main
    trace_and_prune(container=args.container, commands=args.commands, directories_to_prune=args.dirs_to_prune)
  File "/opt/miniconda3/envs/neurodocker/lib/python3.9/site-packages/neurodocker/reprozip/gentle/trace.py", line 86, in trace_and_prune
    raise RuntimeError("Error: {}".format(log))
RuntimeError: Error: NEURODOCKER (in container): ERROR: reprozip trace command exited with non-zero code. Command: /tmp/reprozip-miniconda/bin/reprozip trace -d /tmp/neurodocker-reprozip-trace --dont-identify-packages --continue mri_nu_correct.mni --i /home/T1.mgz --o /home/T1_N3.mgz --n 2