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  1. Before install guest addition from CD, do the following

    sudo apt-get install dkms build-essential linux-headers-generic linux-headers-$(uname -r)

    For missing linux kernel headers or other common problems, refer to this.

    use uname -r or uname -a to look up the kernel version, use dpkg --get-selections | grep linux to check the installed linux kernels.

  2. If you click the sharefolder item in the menubar and get the follwing error: ‘The VirtualBox Guest Additions do not seem to be available on this virtual machine, and shared folders cannot be used without them’, the following commands may be helpful. 

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    sudo apt-get install virtualbox-guest-additions-iso
    sudo apt-get update 
    sudo apt-get dist-upgrade
    sudo apt-get install virtualbox-guest-x11

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  1. Go to virtualbox installation directory and execute the following command:

    D:\Program Files\Oracle\VirtualBox\VBoxManage.exe modifyhd "F:\VirtualBox\my ubuntu.vdi" --resize 15360

    Note 15360 is the new size (M), this command can only enlarge the size.

  2. Install gparted by sudo apt-get install gparted and make the extended disk space available to use.

  3. Remount /home to the new disk. For concrete steps, refer to this link.

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  1. Initialize center and local repository

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    #init from scratch
    git init <local_dir>
    #for central repository without working directory, use --bare
    git init --bare <local_dir>
    #clone from GitHub, can just clone a subdirectory. pull all the remote branches. set up "main" branch to track "origin/main".  
    git clone <remote_repo> <remote_dir>
    #pull from other local repository
    git remote add <remote_repo> <remote_address>
       git pull # only pull the default branch
    git pull <remote_repo> <remote_branch> # pull is equal to fetch and merge
       git fetch <remote_repo> <remote_branch>

  2. Configuration

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    git config --global user.name $name
    git config --global user.email $email
       git config --global credential.helper store
    git config --global alias.$alias-name $git-command
    git config --system core.editor $editor # e.g., vim
    git config --global --edit

    .git/config Repository-specific settings.
    ~/.gitconfig User-specific settings. This is where options set with the —global flag are stored.
    /etc/gitconfig System-wide settings.

  3. Staged snapshot in the staging area
    operations on tracked files:

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    git add <file>
    git add <dir>
    git add . # add all the files in the current directory
    git add * # add  all the files and folders in the current directory 
       # before using `git add .` or `git add *`, we can exclude the untracked files in `.gitignore` (e.g., `*.<ext>`, `<dir>/`, use `!<file>` for exception).

    git rm <file> # delete the file
       git rm --cached <file> # untrack the file


    git mv <old name> <new name> # mv = rm+add

    git restore --staged <file> # move staged changes to unstaged changes
       git restore <file> # remove unstaged changes
       

    #clear the entire staging area
    git reset HEAD # move all staged changes to unstaged changes
       git reset --hard HEAD # remove all staged and unstaged changes

  1. Commit the staged snapshot

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    git commit -m "<message>"  #new commit node
    git commit --amend #old commit node
    #`-a` means staging all the changes of tracked files
    git commit -a -m "<message>" 
    git commit -a --amend

  2. Branch

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    git branch #list local branches		
       git branch -r # list remote branches
       git branch -a # list both remote branches and local branches
       git branch -vv # list local branches and their tracked remote branches	
    git branch -d <old_branch> #use -D enforce delete
    git checkout <old_branch> #switch to branch $branch 
    git branch <new_branch> #create a new branch 
    git checkout -b <new_branch> #switch to a new branch $branch

    (a) Imaging there exists a hash table of key:value pairs with branch name as key and commit node as value. When checkout a new branch b1, b1:current-commit-code will be stored in the hash table. When checkout an existing branch b1, you will reach the hashed commit code. In both cases, b1 (HEAD) will be used as the hash key for the next commit node, that is, when you commit next time, b1:new-commit-code will be updated in the hash table.
    (b) Another perspective is treating the branch name as a pointer to the commit node and each branch is a retrospective history dating back from that node, which is essentially the same as (a).

    When checkout to another branch, git status (staged or unstaged modifications) will be transferred to that branch. If there exists file conflicts (operations on common yet different files), checkout will be forbidden.

    Besides branch, users can also add tag to each commit node.

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    #assume the current branch is master
    #merge: merge experiment into master
    #master moves one step forward, both experiment and original master are its parents
    git merge experiment
    #assume the current branch is experiment
    #rebase: base experiment on master
    #duplicate the nodes between C2 and experiment after master, move experiment to up-to-date
    git rebase master
    #in the simple fast-forward case, assume <branch> is ahead of <branch1>
    #then, `merge <branch1> <branch2>` and `rebase <branch1> <branch2>` work the same, just move <branch1> to <branch2>.
    #whereas, `merge <branch2> <branch1>` or `rebase <branch2> <branch1>` are not allowed.

  3. Tracking changes

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    git status 
    git log #commit history
    git log -n <limit> --stat
       git log --all --graph --oneline # show the tree structure of all branches
    git log --grep="<pattern>"
    git log --author="John Smith" -p hello.py
    git diff #view unstaged modification
    git diff --cached #view staged modification
    git diff <branch1>..<branch2>
    git diff <repo>/<branch1>..<branch2>

    when using git log, it will only show the ancestral commit nodes of current node.

  4. Date back to history

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    #revert the operations in <commit> and add one commit node ahead of HEAD
    #revert does not work on file
    git revert <commit>
    #go back to <commit>
    #git checkout <commit> <file> is just copying the <file> in <commit>
    git checkout <commit>  		
    #git reset <commit> changes branch name, working directory, and staged index
    #git reset <file> is removing the staged file
    git reset --mixed <commit> #default, save the working directory
    git reset --soft <commit> #save both working directory and staged index
    git reset --hard <commit> #save none, dangerous!

    (a) For reset file, there are no options --hard and --soft.
    (b) For reset commit, after reset --mixed or reset --hard, there are no staged snapshots. After reset --soft, staged snapshots enable the staged index to remain the same. More specifically, at the time before or after reset --soft, if you run git commit, the generated commit node should be the same.

  1. Communicate with remote repositories

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    git remote -v #list remote repositories
    git remote add <remote_repo> <remote_address>
    git branch -r #list the fetched branches of remote repositories

    git fetch <repo>  # fetch all of the remote branches
    git fetch <repo> <remote_branch>:<local_branch>
    git checkout -b <new_branch> <repo>/<remote_branch> # Checking out a local copy of specific branch
    git pull <repo> <remote_branch>:<local_branch>
    git push <origin> <local_branch>:<remote_branch>

    after merging code to address the conflict, use git commit -a -m "$message", then git push.

    git pull is equal to a git fetch followed by a git merge.

  2. Clean working directory

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    git clean -f/d #clean untracked files/directory
    git clean -f $path #clean untracked files in $path
    #`git clean` is often used togther with `git reset —hard`

  3. Stashing

    If you are working in your repository, and your workflow is interrupted by another project, you can save the current state of your repository (the working directory and the staging index) in the Git stash. When you are ready to start working where you left off, you can restore the stashed repository state. Note that doing a stash gives you a clean working directory, and leaves you at the last commit. 

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    git stash save # stash the current state
    git stash list # see what is in the Git stash:
    git stash apply # return your stashed state to the working directory
    git stash pop # return your stashed state to the working directory and delete it from the stash

    Note the commit-tree grows. “git log” prints the path from root to current node. “leave behind” prints the path from current node to the first common ancestor between current node and new node. Detached head will be off any branch, so create a new branch for the detached head.

Tips:

  1. checkout and reset work on both file and commit with different meanings and usages, while revert only works on commit.
  2. reset is often used for cancelling uncommited changes while revert is often used for cancelling commited changes.
  3. Compared with reset, checkout and revert focus on the modification, so they are forbidden in many cases.

Github User:

  1. create a repository on GitHub
  2. create a local folder
  3. git init
  4. git remote add <remote_repo> <remote_address>
  5. git pull <remote_repo> <remote_branch>
  6. git push --set-upstream <remote_repo> <remote_branch>
  7. add files
  8. git add *
  9. git commit -m "msg"
  10. git push

Resources:
A good Chinese tutorial for git is here.
A good English tutorial for git is here.

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  1. Remove default OpenJDK

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    sudo apt-get purge openjdk-\*

  2. download jdk(containing jre) and tar.

  3. add into /etc/profile

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    JAVA_HOME="/home/newly/Program_Files/Java/jdk1.8.0_65"
    PATH="$PATH:$JAVA_HOME/jre/bin:$JAVA_HOME/bin"

  4. set newly installed jdk as default jdk.

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    sudo update-alternatives --install "/usr/bin/java" "java" "$JAVA_HOME/bin/java" 1
    sudo update-alternatives --install "/usr/bin/javac" "javac" "$JAVA_HOME/bin/javac" 1
    sudo update-alternatives --install "/usr/bin/javaws" "javaws" "$JAVA_HOME/bin/javaws" 1

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Locate OpenCV:

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pkg-config --modversion opencv //version
pkg-config --cflags opencv //include file path
pkg-config --libs opencv //library path

Uninstall OpenCV:

  1. go to the compile package and make uninstall
  2. if cannot find the compile package, sudo find / -name "*opencv*" -exec rm -i {} \;

Install OpenCV:

For Windows: C++(Visual Studio)

  1. Download latest OpenCV from http://sourceforge.net/projects/opencvlibrary/?source=typ_redirect.
  2. Make a dir named build. Use cmake to generate OpenCV.sln in build.
  3. Click OpenCV.sln and CMakeTargets->INSTALL->build. You can build it in both debug and release modes.
  4. In the environmental variables, add D:\Program Files\OpenCV_3.0.0\build\install\x64\vc11 as OPENCV_DIR, add Path with %OPENCV_DIR%\bin.
  5. Create a OpenCV project. C/C++->General->Additional Include Directories: $(OPENCV_DIR)\..\..\include
  6. Linker->General->Additional Library Directories: $(OPENCV_DIR)\lib
  7. Linker->Input->Additional Dependencies: copy all the lib files. *d.lib means debug mode.

Note that there may be some problems for visual studio to recognize the updated environmental variable. Try to restart the visual studio or recreate the project.

For Linux: install for C++

  1. pre-install packages
    [compiler] sudo apt-get install build-essential
    [required] sudo apt-get install cmake git libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev
    [optional] sudo apt-get install python-dev python-numpy libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libdc1394-22-dev
  2. download the required version on https://sourceforge.net/projects/opencvlibrary/
  3. make and install 
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    mkdir build
    cd build
    cmake ..     //cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local ..
    make
    sudo make install

Tips: if you want to install multiple versions of OpenCV, set CMAKE_INSTALL_PREFIX differently for different versions of OpenCV.

cmake -D CMAKE_BUILD_TYPE=RELEASE \
    -D CMAKE_INSTALL_PREFIX=/usr/local \
    -D INSTALL_PYTHON_EXAMPLES=ON \
    -D INSTALL_C_EXAMPLES=ON \
    -D OPENCV_EXTRA_MODULES_PATH=../opencv_contrib/modules \
    -D PYTHON_EXECUTABLE=/usr/bin/python \
    -D BUILD_EXAMPLES=ON ..

If want to turn off some modules, use -D BUILD_opencv_xfeatures2d=OFF

Switch between different versions of OpenCV:

switch from version 3.2 to version 2.4 shell

switch from version 2.4 to version 3.2 shell

For Linux: Python(Anaconda)

source activate tgt_env
conda install -c https://conda.binstar.org/menpo opencv
spyder

Then try import cv2

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  • Install gst-plugin

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    sudo add-apt-repository ppa:ddalex/gstreamer
    sudo apt-get install gstreamer0.10-*

  • Install gstffmpeg

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    sudo add-apt-repository ppa:mc3man/gstffmpeg-keep
    sudo apt-get update
    sudo apt-get install gstreamer0.10-ffmpeg

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Remote-SSH: Open SSH Configuration File ~/.ssh/config

Host jump-box
HostName
User
Port

Host target-box
HostName
User
Port 22
ProxyCommand ssh -q -W %h:%p jump-box

Remote Explorer

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For Windows

  1. Download Java JDK from http://www.oracle.com/technetwork/java/javase/downloads/index.html and install. Note that JDK contains JRE. Modify the following environment variables:

    • add JAVAHOME D:\Program Files (x86)\Java\jdk1.7.051
    • add Path %JAVA_HOME%\bin;\%JAVA_HOME%\jre\bin;
    • add CLASSPATH %JAVA_HOME%\lib\tools.jar;%JAVA_HOME%\jre\lib\rt.jar

  2. Download Eclipse from http://www.eclipse.org/downloads/ and click eclipse.exe

For Linux

  1. Install JDK

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    sudo add-apt-repository ppa:webupd8team/java
    sudo apt-get update // depending on the needed java version
    sudo apt-get install openjdk-7-jdk
    or sudo apt-get install openjdk-8-jre openjdk-8-jdk

  2. Download Eclipse and unpack

  3. Create a new file eclipse.desktop in /usr/share/applications/ and add the below code 

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       [Desktop Entry]
       Name=Eclipse
    Comment=Eclipse IDE
    Exec=/home/liniu/Program_Files/Eclipse/eclipse/eclipse
    Icon=/home/ivan/Eclipse/icon.xpm
    Categories=Application;Development;Java;IDE
    Type=Application
    Terminal=0

    and then run

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    sudo desktop-file-install /usr/share/applications/eclipse.desktop

  4. Add to the path: sudo ln -s /opt/eclipse/eclipse /usr/local/bin/

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  1. install by running the sh file
  2. refer to the crack folder
  3. After installation, create a shortcut
    a) sudo ln -s /usr/local/MATLAB/R2012a/bin/matlab /usr/bin/matlab
    b) copy the matlab.desktop to /usr/share/applications and matlab.png to /usr/share/icons.

Problem:

  1. /tmp/mathworks……. permission denied

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    $cd /Matlab.R2012a.UNIX/sys/java/jre/glnxa64/jre/bin
    chmod +x ./java

  2. warning: usr/local/MATLAB/R2012a/bin/util/oscheck.sh: /lib/libc.so.6: not found

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    sudo ln -s /lib/x86_64-linux-gnu/libc.so.6 /lib64/libc.so.6

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Format

  1. DICOM: (Digital Imaging and COmmunications in Medicine) meta info + raw data
  2. nrrd: meta info (e.g., sizes, dimension, encoding, endian) + raw data

The meta info in nrrd mainly consists of the format of raw data while the meta info in DICOM contains the detailed information of patient, study, and series.
There exist matlab and python functions to read DICOM and nrdd files.

  • MATLAB

DICOM is generally a directory containing a sequence of slices while nrrd is a single file. The meta info of DICOM is more complicated and thus more error-prone than that of nrrd. Use DICOMPatcher to fix up DICOM files if errors occur when loading them to 3D Slicer.

Software

  1. 3D Slicer: cross-platform, compatible with different formats (e.g., DICOM and nrrd), and convert between them.

  2. Other softwares to view medical images: http://www.cabiatl.com/mricro/dicom/#links