install_mango.md

How to Process MRI Images:

1. Beginner's Guide to Command-Line Interface
2. Installation Instructions
   • Programs
   • Fulton Supercomputing Lab specific instructions
3. Preprocessing T1 images
   • Download example files
   • Convert DICOM to NIfTI
   • Align anterior commissure and posterior commisure
   • Correct intensity nonuniformities (bias field)
   • Resample images to isotropic voxel size 1
   • Brain Extraction and Tissue Segmentation
4. Hippocampus Segmentation
   • Placing Landmarks

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• Firefox
• DICOM Toolkit
• dcm2nii DICOM to NIfTI conversion
• Multi-image Analysis GUI (MANGO)
• MATLAB R2014a
• ACPC Detect
• Git
• CMake
• C++ Compiler
• Advanced Normalization Tools
• ITK
• Convert3D

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The installation guide can be found here. You can either download the latest version (v3.2.1) or previous versions. The current version (v3.2.x) does not seem to run quite like is has in the past, so we are currently using version 3.1.x.

Linux

• Download the latest version here.

• Unzip the downloaded file (which currently produces a folder call mango).

#!console
# unzip /home/<username>/Downloads/mango_unix.zip -d /usr/local/

• Configure Mango

#!console
# /usr/local/Mango/mango

Click Accept

Go to Options > Install Utilities

Location should be: /usr/local

Click Install

You should have the following files:

#!console
$ ls /usr/local/bin/
applytransform  convert2des  genheader  mango    vols2series
convert2avw     convert2nii  imageinfo  resizer
convert2dc      makeroi    roi2nii

You can confirm that the command-line utilities were installed correctly by typing:

#!console
$ mango

Mac

• You can find the downloads page here.

• Open (double-click) the mango installer.pkg to install the program.

• If you want to install command-line options, open the Mango.app and go to Options > Install Utilities… and then click Install. The program automatically installs the folder at /Users//bin/, but you need to move those files in that directory to /usr/bin:

#!
$ sudo mv /Users/<username>/bin/* /usr/bin/
$ rmdir /Users/<username>/bin

Windows

• You can find the downloads page here.

• Extract the mango installer (It doesn't really matter where you extract it to, as long as you can find it later)

• Run mango installer and when prompted to create a shortcut do so

• Place the mango shortcut in a directory and add an environment variable leading to it under PATH (For example, if you placed mango in the "Downloaded Program Files" path you would add ;C:\Windows\Downloaded Program Files to PATH)

• To access mango from the command prompt type start mango