install_cmake.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:

#!console
# cd /usr/local/
# wget http://www.cmake.org/files/v3.0/cmake-3.0.0.tar.gz

• Unzip the downloaded file:

#!console
# tar xzf cmake-3.0.0.tar.gz

• Configure, compile, and install:

#!console
# cd cmake-3.0.0
# ./configure --prefix=/usr/local && make && make install

Mac

• Download the dmg file from here.

• Open the dmg file to run the installer.

• You should only have to drag and drop the app into the Application folder.

• Open the CMake.app and go to Tools > Install For Command Line Use. You will need to make sure you have admin permissions.

• If you get errors, open up the CMake application from terminal:

#!console
$ sudo /Applications/CMake.app/Contents/MacOS/CMake

Windows

• Download the latest version.
• Run the CMake installer (for this version it was referred to as "cmake-3.0.0-win32-x86" in my downloads).

The welcome scree should open. Click Next.

It then shows the license agreement. Click I Agree.

Install options will appear. Select the Add CMake to the system PATH for all users and click next.

Now choose the location you'd like to install CMake.

Now click Install.

• Go to the Installation tab and select Apply Changes