FreeSurfer Version 7 Beta (pre-release)

This page describes the pre-release (beta) version 7 of FreeSurfer. Below are tarballs and RPMs that you can download and install. The purpose of this beta is for users to install and run FreeSurfer on some of their data sets using their computers and their commands and their post-processing to help us track down any errors prior to the full release. To that end, we would like for you to do several tests:

• Do not use the beta version for any analyses that you want to publish. Only use full releases.
• Run recon-all on the various computers (desktops, clusters, etc) that you use
• Run recon-all with any special flags that you might use (eg, expert options)
• Edit the recon and verify that the changes are taken and preserved
• Run recon-all on problem data sets
• Run recon-all on hires data (just add -hires flag), where hires is voxel size less than 1mm
• Run recon-all with T2 or FLAIR input (1mm or hires)
• Run longitudinal recon-all
• Run the subfield analysis (hippcampal subfields, amygdalar and thalamic nuclei). You can do this by just adding -subfields to recon-all
• Run samseg on a data set. We'll have more docs on samseg later, but for now SAMSEG = Sequence Adaptive Multimodal Segmentation can take any modality (or combination) and produce a volume segmentation (seg.mgz, like the aseg.mgz). You can run it with something like "samseg --i inputvolume.mgz --o samsegdir". It should take about 45min. For now, we just want to make sure that it runs on your system.
• Run any special post-processing to make sure that nothing breaks.

We'll update the release notes with new features for the full release, but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make). A new version of Tracula is in the works but probably will not be out until April or so; we'll have a minor release when it is ready.

FreeSurfer Release 7 System Requirements

Summary of Requirements:
Operating Systems:
Linux - we use/test CentOS6, CentOS7, Ubuntu18
MacOS - we use/test 10.13 High Sierra, 10.14 Mojave, 10.15 Catalina
Processor Speed: 2.8GHz or higher
RAM: 8GB for recon, 16GB suggested for viewing graphics
Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers
Size of installed image: 10GB
Typical size of a processed subject: 300MB
Other requirements: Matlab (only needed to run FS-FAST, the fMRI analysis stream)

FreeSurfer 7.0.0 beta 1 Notes

Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions).

Linux install and setup: here.

Mac install and setup: here.