Pradeep,
If you have a Sandy-Bridge or Ivy-Bridge based system, and it has at
least eight cores, and those cores run at 3.4GHz, and you use the
'-openmp 8' flag (available in v5.3) and you arrange recon-all to run
the hemi stages in parallel, then recon-all completes in about 3.5
hours. In the up
Hi Nick,
Can you tell me what would be best processing time to do recon-all process
on one brain mri image using a high end machine ( Servers ) or using GPU
based machine.
We have more than 1000 of brain mri images, processing all these images is
the bottleneck now.
Pradeep
On Tue, Dec 16, 2014
Pradeep,
Our lab will be getting a Haswell-based system soon and will evaluate
any speed gains. The system is a Dell PowerEdge R730 with an Intel®
Xeon® E5‐2643 v3 3.4GHz processor.
N.
On Mon, 2014-12-15 at 13:43 +0530, pradeep mahato wrote:
> Hello everyone,
>
>
> Have anyone used Broadw
Hello everyone,
Have anyone used Broadwell or Haswell process for Brain MRI image
processing.
If used can you please mention the system configuration you are using.
How long does it take to run recon-all process for one brain MRI image.
Thanking you
Pradeep Kumar Mahato
January 18, 2012 10:10 AM
> |To: Bruce Fischl
> |Cc: freesurfer@nmr.mgh.harvard.edu; Malcolm Tobias
> |Subject: Re: [Freesurfer] Performance questions
> |
> |Malcolm,
> |
> |actually, they (IBM) are looking at openmp (to allow multiple threads to
> |process for-loops) and SSE3
[mailto:ni...@nmr.mgh.harvard.edu]
|Sent: Wednesday, January 18, 2012 10:10 AM
|To: Bruce Fischl
|Cc: freesurfer@nmr.mgh.harvard.edu; Malcolm Tobias
|Subject: Re: [Freesurfer] Performance questions
|
|Malcolm,
|
|actually, they (IBM) are looking at openmp (to allow multiple threads to
|process for
Malcolm,
I think it will be at least 10% faster. I messed with the Intel
compiler a couple years ago, but they wanted to charge a yearly fee for
its usage (mgh doesnt qualify as an academic user), so we nixed using
that compiler. also, fyi, I was unable to get the AMD compiler to build
the code
Pedro,
I've got a run going with the Intel compilers now (I'm assuming that's what
you meant?). Besides producing faster code, it will be interesting to see
whether the compilers have a noticeable result on the results.
Malcolm
On Wednesday 18 January 2012 12:14:42 Pedro Paulo de Magalhães O
OpenMP (depending how efficiently FreeSurfer can be parallelized) would be a
great benefit here.
I have no idea what's causing the centos4 vs. 5 results, but it might be
interesting to start collecting some performance data if enough people are
interested.
All the benchmark numbers I've menti
I think IBM has a better compiler. Better than gcc and slightly slower
than intel compiler
Sent from my iPad
On Jan 18, 2012, at 16:09, Nick Schmansky wrote:
> Malcolm,
>
> actually, they (IBM) are looking at openmp (to allow multiple threads to
> process for-loops) and SSE3 instructions (bette
Malcolm,
actually, they (IBM) are looking at openmp (to allow multiple threads to
process for-loops) and SSE3 instructions (better vectorization).
recon-all --help contains some timings for an AMD processor. centos4
vs. centos5 itself should not account for any speed differences, but it
is true
Hi Malcolm
in collaboration with IBM we are also looking at MPI and pthreads.
cheers
Bruce
On Fri,
13 Jan 2012, Malcolm Tobias wrote:
>
> Is there a standard benchmark for FreeSurfer?
> I've been using the data under subjects (Bert?/Ernie?) and running a recon-
> all:
>
> recon-all -s ernie -i
Is there a standard benchmark for FreeSurfer?
I've been using the data under subjects (Bert?/Ernie?) and running a recon-
all:
recon-all -s ernie -i ./sample-001.mgz -i ./sample-002.mgz -all
On our hardware using the 5.1 distributed binary (freesurfer-Linux-
centos4_x86_64-stable-pub-v5.1.0.tar
Hi Chris,
it depends on where the tumor is and how big it is. It it's within the wm
you could certainly just fill it as a wm edit and things should work.
cheers
Bruce
On
Fri, 12 Mar 2010, Chris Filo Gorgolewski wrote:
> Hi,
> how does freesurfer perform on brains with tumor? Are the any specyf
I think the results may be quite unpredictable. It depends on the size of
the tumor, the infiltration, the necrosis, etc.
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.4 www.Netf
Hi,
how does freesurfer perform on brains with tumor? Are the any specyfic
options that could improve the results (like masking for example)?
Cheers,
Chris
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Stephen,
The 30 minute estimate for the -autorecon1 stage is no longer accurate.
It got slower when we added a feature to improved the skull-strip step.
The feature is to make use of an atlas to determine where skull and
cerebellum might be. To use that atlas requires a registration to that
atlas
Hi all. Documentation estimates 30 minutes for -autorecon1 on the
sample data provided with the most recent freesurfer release. Our 2008
iMac with 4GB of RAM takes about 90 minutes. Throughout the job CPU
utilization was high but there was plenty of free RAM.
Is 90 minutes common for similarly equ
well, you could buy a faster machine :). The 6 days I don't think is
normal. The subcortseg can take a long time, although on current opterons
it's more like 15 hours I think. Check to make sure that you don't have a
cerebellum attached in your filled volume (or ?h.orig surfaces), and that
the
Hello
We are running freesurfer on a Power Mac G4 with a 1.25 GHz
processor and 1 GB Ram.
The subcortical segmentation procedure recon-all subcortseg –s ran for 49
hours.
The rest of autorecon2 (recon-all –autorecon2-cp –s ) has been
running for 6 days and is still working on t
Hi Adam,
we really have spent next to no time optimizing, but I'm suprised the
dual xeon isn't significantly faster than your pIII.
On Mon, 22 Mar 2004,
Adam Thomas wrote:
>
> Has anyone done any performance benchmarks on recon-all recently? I've
> been running it on one of our newer machines
Has anyone done any performance benchmarks on recon-all recently? I've
been running it on one of our newer machines (dual Xeon 3.06 GHz, 2GB ram,
6121 bogomips) and it still takes about 90 minutes to do finalsurfs on one
hemisphere. Which is the same time the help file quotes for a 1 GHz
Pentium I
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