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

• 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

Installation instructions can be found here: http://support.dcmtk.org/docs/file_install.html

Linux

• Download the latest version of dcmtk:

#!console
# cd /usr/local/
# wget ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/dcmtk360/dcmtk-3.6.0.tar.gz

• Extract Archive

#!console
# tar xvzf dcmtk-3.6.0.tar.gz

• Configure:

#!console
# cd dcmtk-3.6.0
# ./configure

#!console
# make all

• Install the executables and some support files (data dictionary):

#!console
# make install

Mac

Windows