[Camino-users] sfpeaks

[Yan Jin]

Hi Mara and Kiran,

Thank you so much for your kindly replies! Okay, the default value for
-density is 1000. When I reduced it to 100, I got it done within an
hour or so with the pig brain data (I believe that all the commands I
typed were right since I just copied and pasted from the website.).
But three hours is not possible for my computer with the default
setting. Our data set is 128x128x55. I used density=300. I left it run
and went to bed last night. When I got up this morning, it was done.
So I think that it got done within 10 hours or so. My computer has a
single QuadCore CPU (Intel  i7 @ 3.40 GHz with 16 GB RAM). My
questions are:

1. Based on your experience, what typical value do you use for
-density? Is 1000 necessary?

2. Also, there are some other parameters that you can tune, such as
-numpds, -searchradius, -pointset. Do they affect the running time as
much as -density do? Do pointset overrides density? What is the
default value for -pointset?

Thanks,
Yan

On Wed, Dec 14, 2011 at 8:43 AM, Cercignani, Mara
<m.cercignani at ucl.ac.uk> wrote:
> hello,
>
> That depends a lot on what type of computer you're using...anyway I can tell you that in my experience (and on the computer I use which has a double QuadCore processor E5630)  a dataset of 96x96x60 takes about 20 hours - so I guess the pig brain data, which is 128x128x10, should take about 1/4 of that time, i.e. 5 hours.
>
> Mara
>
On Wed, Dec 14, 2011 at 1:38 AM, Seunarine, Kiran <k.seunarine at ucl.ac.uk> wrote:
> Hi Yan,
>
> I would expect sfpeaks to finish within about 1-3 hours (certainly no longer than a day).  As far as I can see, the sfpeaks command you used looks correct.  Please send the list of commands you used to generate pigBrainODFs_SH4_PDs.Bdouble and I'll try and work out why this step is taking so long.
>
> Best regards,
>
> Kiran
>> ________________________________________
> From: camino-users-bounces at www.nitrc.org [camino-users-bounces at www.nitrc.org] on behalf of Yan Jin [yjinz at umich.edu]
> Sent: 14 December 2011 01:53
> To: camino-users at www.nitrc.org
> Subject: [Camino-users] sfpeaks
>
> Hi,
>
> I am new to Camino... I wanted to use sfpeaks to process our q-ball
> imaging data; however, it seems to take extremely long time to run it.
> In fact, I have never seen it finished. I used the example in
>
> http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Tutorials.QBallTutorial
>
> and type:
>
> sfpeaks -inputmodel sh -order 4 -numpds 3 < pigBrainODFs_SH4.Bdouble >
> pigBrainODFs_SH4_PDs.Bdouble
>
> It runs forever... Does anyone know how long it takes to run such a
> simple data set? I downloaded the latest camino version r1018.
>
> Thanks,
> Yan
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