How to analyze the DICOM files from a MRI scan. I had access to a set of MRI scan data, and I wanted to output them to a 3D file to view the innards of the human body. I couldn't get the online tutorials(from instructables and sculpteo- both in the References section) working word-for-word, so I will document my steps here. (though it is extremely unlikely that I will once again be analyzing a MRI scan data.)

get the latest version of MRIcron/NPM/dcm2nii. Open the app dcm2niigui, and select File > DICOM to NIFTI. Navigate to the directory with the data(in my case it was the directories named SE000000~SE000017), and click open. It should convert the files into something with .nii.gz extension.

must have XQuartz to run, and must execute

$ export FREESURFER_HOME=/Applications/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

in the terminal(or write it to ~/.profile) to run the app.

run $ recon-all -s output -all -notal-check -i <???.nii.gz> -sd <~/output_directory> -cw256

Change the stuff inside < > to your configuration. It takes time. (The app told me to add options -cw256 and -notal-check to process them properly, but I don't really know what they are for.)

$ mris_convert <??.pial> <??.stl>

FAQ- FreeSurfer

Q. Help! I got this error message: "mri_watershed error: GLOBAL region of the brain empty!" - what should I do?

A: Run this:
recon-all -skullstrip -no-wsgcaatlas -s <subjid>

If that goes through without error, you can finish processing your data by running:
recon-all -autorecon2 -autorecon3 -s <subjid>

• FreeSurfer Beginners Guide
• 3D PRINT YOUR OWN BRAIN- -instructables
• How to: 3D print your own brain using MRI or CT scans & free software -sculpteo