I suspect this issue has much more to do with the OS, the local file system, and the network file system and how the 3 interact. It can get very complicated. I have written several scrips that use spm_read_vols (including time series analysis) over network file systems. Work great on a 64bit linux server reading files using NFSv4 and with the server using XFS for the local file system. On Wed, Jul 27, 2011 at 5:08 PM, John Ashburner <[log in to unmask]> wrote: > I never use spm_read_vols myself. Are the nifti routines any faster? > > N=nift('file.nii'); > tic = X=N.dat(:,:,:,:); toc > > It's unlikely that we're going to re-code this stuff to make it work > faster on the kind of device we don't have access too. > > Best regards, > -John > > > On 27 July 2011 22:00, Welsh, Robert <[log in to unmask]> wrote: >> Hi authors of SPM8, >> >> I've noticed a horrendous performance hit when accessing time-series data >> when that data sits on a NAS device. >> >> Let's call it an SPM8 x NAS interaction. >> >> If I read the 4D dataset with spm_read_vols from our 48TB NAS it takes >> about 250 seconds, however if I read that 4D dataset with some homegrown >> matlab code to just open the file, skip over the header and read the data >> in, then it only takes about 2.5 seconds, or 100 times shorter! This is on >> the exact same file on the exact same NAS device. When I run spm_read_vols >> through the system profiler of course the time is pretty much evenly split >> between spm_matrix and spm_slice_vol. The impact on our throughput is >> high, that is processes are being IO limited when indeed they should not >> be. In fact for some custom functional connectivity processing I forego >> the use of the spm_read_vols to get my time-series data. >> >> Can I ask the authors to examine writing a different piece of code for >> reading time-series data that could jump around the spm_slice_vol and >> spm_matrix given that the data has to already be resliced on disk and thus >> the application of spm_matrix maybe is redundant, if having statistics >> performed? Given that NAS devices are becoming more popular it seems that >> this will be having an impact for others eventually. >> >> I've seen this on both linux and mac os x systems running both matlab 2007 >> and matlab 2009. >> >> Have others noticed this issue? >> >> -Robert Welsh >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues >> >