install_acpcdetect.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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Linux

• Download the latest version here.

• Unpack the package:

#!console
# cd /usr/local/
# mkdir art
# cd art/
# mv /home/<username>/Downloads/acpcdetect.tar.gz /usr/local/art/
# gunzip acpcdetect.tar.gz
# tar xvf acpcdetect.tar
# mv /usr/local/art/acpcdetect /usr/local/bin/

• Set the environmental variables:

#!console
$ ARTHOME=/usr/local/art
$ export ARTHOME

• You can confirm that the program was installed correctly by typing:

#!console
$ acpcdetect

Mac

Only available for Linux systems.

Windows

Only available for Linux systems.