FreeSurfer System Requirements
Summary of Requirements:
Operating System: Linux (CentOS 7, 8, Ubuntu 18, 20, 22), Mac OS 10.15 or newer, Windows 10,11 (hosting Linux under WSL or VirtualBox)
Intel processor supporting AVX instructions
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: 16GB
Typical size of a processed subject: 300MB
Other requirements: Matlab (only needed to run FS-FAST, the fMRI analysis stream)
Freesurfer is available for the Linux and Mac OS X operating systems. It can also be used on Windows with the Windows Subsystem for Linux (WSL) or VirtualBox hosting Linux (but runs a bit slower). The download page lists the supported platforms and we have a public VM including instructions about how to setup VirtualBox and WSL. Matlab is required to run the FS-FAST component of Freesurfer (but Matlab is not required to run the reconstruction utilities).
A processor with at least 2 cores, e.g., Intel i5, i7, i9 chip, each with a speed of 2GHz or faster is recommended. Freesurfer is highly CPU and memory intensive (and moderately disk intensive), so concentrate on boosting those performance aspects (more memory is better...16GB is highly recommended! especially if you are hosting linux on Windows with WSL or Virutalbox).
With the inclusion of new OpenMP-enabled code in freesurfer, multiple-cores can now be accessed by recon-all. This means you should also consider purchasing a multi-core machine if you intend to process multiple subjects at the same time. If you do this, be sure to purchase 4GB per subject, that is, if you would like to process four subjects at once, your machine must have four cores and 16GB of memory. The flag you would include with recon-all to do this is: -openmp 4 which tells recon-all to use four cores (cpus) when the special parallelized code is run (ie. the 'gcareg' stage).
Most modern video graphics card will perform fine, but be aware that graphics cards that use CPU memory as video memory will have a noticeably slow redraw rate. NVidia graphics cards have been found to work best with freesurfer. While freesurfer includes some GPU support, it is not actively supported anymore, so purchasing a GPU card explicitly for freesurfer is not recommended, in lieu of purchasing multiple cores and using the OpenMP functionality (-openmp <num_threads> flag). A 19" (or greater!) monitor is also recommended.
If you're running Freesurfer on a server, then allocate 4GB of memory to your job.
Freesurfer requires about 10GB of disk space for the full installation, which includes the Freesurfer binaries, support libraries, the MINC toolkit, and sample MRI data.
The volume and surface data files produced by Freesurfer for a typical subject (assuming two structural MRI scans of source data) consume about 370MB of disk space. The full tutorial dataset is about 50GB.
Mailing list notes regarding suggested specs for a Linux box:
- CPU: Intel vs AMD: no preference. also, CPU speed is not critical. It is better to have at least 4GB, and budget 4GB per subject you want to process simultaneously. Try to get an 'Ivy Bridge' motherboard architecture or whatever is newer. This allows better addressing of scattered memory which is common in freesurfer, and it alone accounts for a 5% or so speedup. AMD might have a similar memory controller.
- Graphics card:
- ATI (AMD) vs nVidia: We still spec nVidia because we don't have problems with its OpenGL-X driver under linux. Perhaps ATI has finally supplied one that works, but this hasn't been attempted in a couple years. ATI cards on the Mac work fine with freesurfer though.
- GPU: We no longer support [further] CUDA or GPU development because of lack of resources and difficulty, in preference to using OpenMP, which uses CPU cores. We will continue to support the existing GPU CUDA code that runs on recon-all with the -use-gpu switch. By support, keeping it running with each new nvidia cuda driver release as best as we can.
- Disk: Freesurfer is not disk intensive, so SSD is not a benefit. Budget 400MB per subject for storage.
- Linux: Both freesurfer and fsl groups use CentOS 6 in our Centers. It seems to work well.