install_convert3d.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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Convert3D requires several programs to be installed first: cmake and ITK. You can double check that cmake was installed:

#!console
$ cmake --version

Linux

• Download the latest version of Convert3D:

#!console
# cd /usr/local/
# wget http://sourceforge.net/projects/c3d/files/latest/download

• Extract Archive

#!console
# tar xvzf c3d-nightly-Linux-x86_64.tar.gz

• Configure Convert3D:

#!console
# mv -i /usr/local/c3d-1.0.0-Linux-x86_64/bin/* /usr/local

Mac

• Download the latest version of Convert3D:

#!console
# cd /usr/local/
# wget http://sourceforge.net/projects/c3d/files/latest/download

• Run the installer

Windows