# How to speed-up FreeSurfer's recon-all?

**URL:** <https://ask.cyberinfrastructure.org/t/how-to-speed-up-freesurfers-recon-all/2788>\
**Category:** Q&A\
**Tags:** image-processing, researcher\
**Created:** [May 15, 2023, 7:42pm UTC](https://ask.cyberinfrastructure.org/t/how-to-speed-up-freesurfers-recon-all/2788 "2023-05-15T19:42:13Z")\
**Posts on this page:** 1\
**Showing post:** 4

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**Author:** ![mitchellxh](https://ask.cyberinfrastructure.org/user_avatar/ask.cyberinfrastructure.org/mitchellxh/32/1033_2.png) [@mitchellxh](https://ask.cyberinfrastructure.org/u/mitchellxh)\
**Post date:** [May 27, 2023, 5:16pm UTC](https://ask.cyberinfrastructure.org/t/how-to-speed-up-freesurfers-recon-all/2788/4 "2023-05-27T17:16:30Z")

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Great question!

Within FreeSurfer, ‘recon-all’ is the command and oft-mentioned workflow for structural reconstruction of brain MRI. This processing stream is limited to only processing a single brain at-one-time. Therefore using traditional parallelization on a cluster is a perfect fit, that is, submitting 10’s to 100’s of ‘recon-all’ jobs at once.

A typical ‘recon-all’ job with 1-core will take 5-6 hours. This probably doesn’t matter to the researcher who needs to process 10’s to 100’s of brains. However, in cases where they may need to process a single brain (or have seemingly unlimited resources…) they can speed-up the individual runtimes with these flags.

Briefly, because ‘recon-all’ splits the brain into 2 hemispheres for reconstruction, it is forced to sequentially process the left-hemisphere and then the right-hemisphere. The developers recognized this bottleneck and added support for Open-MP framework. By simply adding the above flags and allocating across 4 cores (2-cores per hemisphere), the ‘recon-all’ job will now take 3-4 hours.

Hope this adds more context!  
-Mitch

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