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Use of parallelization depends upon the order of how the data needs to be processed.  The recon-all command is not  single command, but a wrapper command that runs a sequence or pipeline of many lower level freesurfer commands in a certain order.   It’s not unexpected for recon-all of the subject bert data to take ~8 hours on a consumer (non-server, non-cluster), stand-alone machine, e.g. recent Intel I9 chip with 8 physical (performance) ~3 GHz cores, 8 virtual cores, 32G of DDR4 RAM and an SSD drive.  If you have access to a computing cluster, you could try running recon-all there - which should reduce the processing time.

- R.

On Apr 3, 2024, at 14:58, Camargo, Aldo <ACamargo@som.umaryland.edu> wrote:

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Hi there,

I was wondering if there is support for GPU on FreeSurfer. I really would like to use it on GPU because is taking 9 hours per subject to recon-all.

Thanks a lot and have a nice day,

Aldo Camargo
Senior Postdoctoral Fellow at the University of Maryland, Baltimore


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