FSL installation in Google colab

fsl-installation-in-google-colab.ipynb

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  "metadata": {
    "colab": {
      "name": "FSL installation in Google colab",
      "provenance": [],
      "collapsed_sections": [],
      "authorship_tag": "ABX9TyPQy2FepmlnrIBzeKsjPPxZ",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/gist/vfmatzkin/7987a6edf034d28427696e1fabbb2979/fsl-installation-in-google-colab.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "51eIk8m-ljpZ"
      },
      "source": [
        "Here I leave a little snippet on how to install FSL in colab. \n",
        "I realized that the installation failed when it tried to run \"file ..\" in order to determine the temporal downloaded tar.gz filetype, so installing 'file' will fix that up.\n",
        "\n",
        "The installation process can take up to 10 minutes."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "DvwX9svW7W4Q",
        "outputId": "9d2077bd-dd46-432d-9f6c-b0d9ee6bd5c3"
      },
      "source": [
        "import os\n",
        "\n",
        "!sudo apt -qq install file\n",
        "!wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py\n",
        "!python2 fslinstaller.py\n",
        "\n",
        "fslpath = \"/usr/local/fsl\"\n",
        "os.environ[\"FSLDIR\"] = fslpath\n",
        "os.environ[\"PATH\"] += os.pathsep + os.path.join(fslpath, 'bin')\n",
        "!. ${FSLDIR}/etc/fslconf/fsl.sh\n",
        "\n",
        "!flirt -version"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "The following additional packages will be installed:\n",
            "  libmagic-mgc libmagic1\n",
            "The following NEW packages will be installed:\n",
            "  file libmagic-mgc libmagic1\n",
            "0 upgraded, 3 newly installed, 0 to remove and 16 not upgraded.\n",
            "Need to get 275 kB of archives.\n",
            "After this operation, 5,297 kB of additional disk space will be used.\n",
            "debconf: unable to initialize frontend: Dialog\n",
            "debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76, <> line 3.)\n",
            "debconf: falling back to frontend: Readline\n",
            "debconf: unable to initialize frontend: Readline\n",
            "debconf: (This frontend requires a controlling tty.)\n",
            "debconf: falling back to frontend: Teletype\n",
            "dpkg-preconfigure: unable to re-open stdin: \n",
            "Selecting previously unselected package libmagic-mgc.\n",
            "(Reading database ... 145483 files and directories currently installed.)\n",
            "Preparing to unpack .../libmagic-mgc_1%3a5.32-2ubuntu0.4_amd64.deb ...\n",
            "Unpacking libmagic-mgc (1:5.32-2ubuntu0.4) ...\n",
            "Selecting previously unselected package libmagic1:amd64.\n",
            "Preparing to unpack .../libmagic1_1%3a5.32-2ubuntu0.4_amd64.deb ...\n",
            "Unpacking libmagic1:amd64 (1:5.32-2ubuntu0.4) ...\n",
            "Selecting previously unselected package file.\n",
            "Preparing to unpack .../file_1%3a5.32-2ubuntu0.4_amd64.deb ...\n",
            "Unpacking file (1:5.32-2ubuntu0.4) ...\n",
            "Setting up libmagic-mgc (1:5.32-2ubuntu0.4) ...\n",
            "Setting up libmagic1:amd64 (1:5.32-2ubuntu0.4) ...\n",
            "Setting up file (1:5.32-2ubuntu0.4) ...\n",
            "Processing triggers for man-db (2.8.3-2ubuntu0.1) ...\n",
            "Processing triggers for libc-bin (2.27-3ubuntu1.2) ...\n",
            "/sbin/ldconfig.real: /usr/local/lib/python3.6/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link\n",
            "\n",
            "--2021-01-18 22:37:15--  https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py\n",
            "Resolving fsl.fmrib.ox.ac.uk (fsl.fmrib.ox.ac.uk)... 129.67.248.65\n",
            "Connecting to fsl.fmrib.ox.ac.uk (fsl.fmrib.ox.ac.uk)|129.67.248.65|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 100244 (98K) [application/octet-stream]\n",
            "Saving to: ‘fslinstaller.py’\n",
            "\n",
            "fslinstaller.py     100%[===================>]  97.89K   250KB/s    in 0.4s    \n",
            "\n",
            "2021-01-18 22:37:16 (250 KB/s) - ‘fslinstaller.py’ saved [100244/100244]\n",
            "\n",
            "\u001b[1m--- FSL Installer - Version 3.0.21 ---\u001b[0m\n",
            "When asked a question, the default answer is given in square brackets.\n",
            "Hit the Enter key to accept this default answer.\n",
            "Where would you like the FSL install to be (including the FSL folder name)? [/usr/local/fsl]: \n",
            "Downloading...\n",
            "Checking FSL package\n",
            "\u001b[92m[OK] \u001b[0mFile downloaded\n",
            "Installing FSL software version 6.0.4...\n",
            "-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b|\b/\b-\b\\\b\u001b[92m[OK] \u001b[0mFSL software installed.\n",
            "|\bPerforming post install tasks\n",
            "/\bPatching asl_gui for fsl 6.0.4\n",
            "Stage 1\n",
            "By installing this python distribution you agree to the license terms in\n",
            "/usr/local/fsl/fslpython/LICENSE.txt\n",
            "100%\n",
            "Stage 2\n",
            "100%\n",
            "/tmp/fslpython6fph/fslpython_miniconda_installer.log\n",
            "configure_eddy.sh: /usr/local/fsl/bin/eddy NOT detected. Checking for /usr/local/fsl/bin/eddy_openmp.\n",
            "configure_eddy.sh: /usr/local/fsl/bin/eddy_openmp detected. Creating symlink to /usr/local/fsl/bin/eddy now.\n",
            "configure_eddy.sh: /usr/local/fsl/bin/eddy_cuda NOT detected. Checking for specific eddy_cudaX.X versions now.\n",
            "configure_eddy.sh: found eddy_cuda versions... /usr/local/fsl/bin/eddy_cuda8.0 /usr/local/fsl/bin/eddy_cuda9.1\n",
            "configure_eddy.sh: checking /opt/cuda* for installed cuda versions\n",
            "configure_eddy.sh: no cuda found in /opt/cuda (or no access)\n",
            "configure_eddy.sh: checking /usr/local/cuda for installed cuda versions\n",
            "configure_eddy.sh: found cuda versions: /usr/local/cuda /usr/local/cuda-10.0 /usr/local/cuda-10.1\n",
            "Post install setup complete\n",
            "\u001b[92m[OK] \u001b[0mPost installation setup complete\n",
            "FLIRT version 6.0\n"
          ],
          "name": "stdout"
        }
      ]
    }
  ]
}