neurolabusc / applesiliconforneuroimaging

Review the challenges and potential of ARM-based Apple Silicon macOS for brain imaging research

I am the endowed chair for brain imaging at the University of South Carolina in the Department of Psychology. I lead the Neuroimaging Core and am the Co-Project Lead for Center for the brain health project of the Center for the Study of Aphasia Recovery. I lead the development of the NiiVue neuroimaging visualization project.

I helped create and lead development of several popular GitHub repositories:

• dcm2niix converts complicated and manufacturer-specific medical imaging data into the simpler NIfTI format popular in neuroimaging sciences. This converter extracts BIDS sequence details that allow reproducible science and curated data. The permissive license and minimal dependencies have led it to be included with many popular tools in the field.
• MRIcron is a light-weight and popular cross-platform visualization tool for neuroimaging.
• MRIcroGL uses the capabilities of modern graphics cards to generate compelling volume rendering visualizations of voxel-based images.
• Surfice uses the capabilities of modern graphics cards to generate compelling surface rendering visualizations of mesh-based data.
• nii2mesh converts voxel-based images to surface meshes and is can be used from a web page without requiring any software to be installed.
• NiiVue is a modular visualization tool for neuroimaging meshes and volumes. It can be inserted into web-pages supporting cloud interface, edge computing and stanalone applications. I am co-originator and co-lead development with @hanayik.

applesiliconforneuroimaging's Issues

tracking docker support for apple m1

thanks for this excellent repository. i wanted to make this issue to indicate that docker has preliminary support for docker. i'm not asking that the readme be updated, but perhaps this issue can be used to track docker support on apple m1.

https://docs.docker.com/docker-for-mac/apple-m1/

note from link above:

Docker Desktop on Apple M1 chip is still under development. We recommend that you do not use tech preview builds in production environments.

Updates on support programmes

Thanks a lot for that great post!

Are there any updates if FSL and AFNI can be now easily installed and used on the M! chip? I think FSL works fin now.
What about nibabel, FMRIPREP, ciftify and freesurfer?

Best,

Julia natively supports Apple ARM and generic ARM

From their downloads page, Julia is now distributed on Apple ARM as well as generic ARM for Linux, amongst others.

• Windows (64-bit [native, portable]) (32-bit [native, portable])
• macOS x86 (Intel or Rosetta) (64-bit [.dmg, .tar.gz])
• macOS (Apple Silicon) (64-bit [.dmg, .tar.gz])
• Generic Linux on x86 (64-bit [glibc, musl]), 32-bit)
• Generic Linux on ARM 64-bit (AArch64)
• Generic Linux on PowerPC (64-bit [little endian])
• Generic FreeBSD on x86 (64-bit)

Docker now runs natively on Apple Silicon

"Docker, a popular multi-platform application used by software developers, has released a version that runs natively on Apple Silicon hardware, including Macs released with Apple's custom-designed M1 chip."

From this article: https://arstechnica.com/gadgets/2021/04/popular-software-development-tool-docker-gets-apple-m1-support/

Opencv

Hi I read that this repository shows which modules work on the new m1 chip, I have been having a ton of issues installing opencv-python inside my Conda venv. but I found a solution so I just wanted to put the following command here in case you want to add it:
conda install -c menpo opencv

MeVisLab updates

Hi,
I was trying to install MeVisLab on my M2 laptop and unfortunately found it unsupported unless with Rosetta. I think the information could be useful for other users. May I know where I can contribute it to this forum? Thanks.
Best wishes
teddy