Hi, I am new to brain medical image analysis. I am running recon-all from freesurfer on my ubuntu virtual machine installed on windows. it takes too much time for single volume of brain. more than 24 hours. Is there something wrong with my installation or it is due to less RAM etc.
Can I use free surfer with GPUs?
Hi @Hassan_Mahmood. What sort of resources do you have? I generally expect FreeSurfer without any parallelization to take ~12 hours on a decently well-powered machine. If you’re seeing 24 hours, I would guess that either you have limited resources (e.g., if you’re on a desktop with other things running, you might be forced to swap memory to disk, which will slow things down considerably) or that your image is low quality, making the topological correction take a particularly long time.
If you do have resources, you can use the
-openmp <N> options to indicate that you want to use multi-processing. Note that if you use both, there may be times when up to 2N threads will be running, and you may see competition for space slowing things down.
thanks @effigies . I will try by those options or upgrading my system.