Dear Volkmar and SPMers
Regarding this post,
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0704&L=SPM&P=R3600&I=-3
>
> I've just investigated this because I am doing a transition of our network filesystem away from NFS and had to resolve some performance issues as well.
As our data continue to grow, I was thinking about having a storage server and mount the data through NFS. This way, I can keep adding more hard drives onto a storage server if necessary. I was wondering if there is any particular reason why you decided to move away from NFS. If you have a better solution to manage storage server, please let me know. All of our machines are linux based, and they are connected through gigabit but my experience with NFS has been pretty slow ~15MB/sec. I tried jumbo frame and etc, but had not luck to reach ~40MB/sec.
This is probably too slow to carry out SPM analysis over NFS isn't it?
With regards,
Hedok
----- Original Message -----
From: Volkmar Glauche <[log in to unmask]>
Date: Thursday, April 5, 2007 3:42 am
Subject: Re: SPM5 slower with 4D files
To: [log in to unmask]
> Hi Jerome,
>
> yes, SPM will probably slower on 4D files than on 3D files. Also
> it will
> be slower on .nii files than on .hdr/.img pairs. The reason is,
> that for
> combined header and data files (as in 3D .nii and 4D cases) SPM
> needs
> something like random-write-access to your file to store small
> bits of
> information. This is more expensive in terms of I/O time
> (especially on
> large disks/RAID systems/network file storage) than storing 3D
> data with
> separate .hdr/.img files. However, storing one large file is more
> efficient in terms of disk usage (if you have
> partitioned/formatted your
> disk to efficiently store large files). In short, there is no free
> lunch, and you have to decide what is more important to you:
> saving
> time or saving disk space...
> I've just investigated this because I am doing a transition of our
> network
> filesystem away from NFS and had to resolve some performance
> issues as
> well.
>
> Volkmar
>
> On Wed, 4 Apr 2007, Paul Macey wrote:
>
> > Hi Jérôme
> >
> > I just wrote something to split 4D to 3D; run the attached
> script
> > (cspm_im_4Dto3D, from SPM5 only) and it will prompt for a 4D
> file to split.
> > You can also use it in batch mode with a couple more options
> (see help). The
> > 3D files should be the same as in the 4D file, so I don't think
> you will
> > loose anything by converting.
> >
> > Best wishes,
> > Paul
> >
> > Jérôme Redouté wrote:
> >> Dear SPMers,
> >> My parameters estimation process is extremely slow. Could
> this slowness
> >> be due to using a 4D-Niftii dataset?
> >> In order to check that, I would like to convert my sw_xxxx.nii
> 4D files
> >> into a set of 3D files.
> >> My questions are:
> >> -SPM has a function to convert 3D -> 4D , but is the reverse
> function>> available? Where can I find such a converter?
> >> -These images are preprocessed (realignment, normalisation,
> smoothing), do
> >> I risk to lose these parameters by converting to 4D to 3D?
> >> Thanks for your help
> >> Jerome
> >>
> >
>
> --
> Volkmar Glauche
> -
> Department of Neurology [log in to unmask]
> Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
> Breisacher Str. 64 Fax 49(0)761-270-5416
> 79106 Freiburg http://fbi.uniklinik-freiburg.de/
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