install_dcm2nii.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

---

• 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

---

The installation guide can be found here.

Linux

• Download the latest version.

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

• Configure dcm2nii

#!console
# mv /home/<username>/Downloads/mricron/ /usr/local/
# ln -s /usr/local/mricron/dcm2nii /usr/local/bin/

Mac

• Download the latest version.

• The zip file should automatically unzip and create a folder labeled osx in your Downloads folder or wherever your files automatically download.

• Move (drag and drop) the osx folder into your Applications directory.

• You can either launch the program directly from the terminal by typing the following:

#!console
$ /Applications/osx/dcm2nii

• If you want to be able to just type dcm2nii into your Terminal window, you can configure the program:

#!console
$ sudo ln -s /Applications/osx/dcm2nii /usr/bin/

Windows

• Download the latest version.

• Unzip the files to C:\Windows\Downloaded Program Files (which produces a folder titled "mricron").

• Edit environment variables to open mricron files from command prompt.

Open Control Panel under the start menu > System and Security > System > Advanced system settings > Environmental Variables

Under System Variables select PATH and edit

Enter ;C:\Windows\Downloaded Program Files\mricron