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Dear SPMers, I have some questions about realignment in SPM96. According to John Ashberner's suggestions given in last June (please see below), when I realign PET images in SPM96, I do it twice. But I am a bit confused by *.mat files generated in realignment procedure. When I do the 1st realignment, I choose: 1) Coregister and reslice 2) Sinc interpolation 3) Mean images only 4) Mask the images The results I get are: mean*01.img(hdr) and a set of *.mat files. Then I go to the 2nd realignment by using mean*01.img(hdr) and the original pet images *.img(hdr): 1) Coregister and reslice 2) Sinc interpolation 3) All images + Mean image 4) Mask the images This time the results I get are: meanmean*01.img(hdr), a set of r*.img(hdr) and a new set of *.mat files. In spm_realign.m, there is one sentence as follows: "Note that if the coregistration is performed more than once on the unresliced data, the starting estimates are obtained from parameters stored in the '*.mat' files." In my case, the coregistration is performed twice on the unresliced data (because the 2nd realignment also uses the original image sets), so the *.mat files obtained from the 2nd realignment are based on the *.mat files from the 1st realignment?? But the 2nd realignment also uses the original pet images with a reference (mean*01.img) different from the 1st one's (*01.img), why need the starting estimates of the 2nd realignment to be obtained from '*.mat' files generated by the 1st realignment? For some reason, for some data set, before I do the 2nd realignment, I delete the '*.mat' files obtained from the 1st realignment, would this action affect the resulting r*.img(hdr) files and meanmean*01.img(hdr)?? And how much is it do you think? The generation of '*.mat' files is a new feature in SPM96. From SPM96 help I know that it is not necessary to get r*.img(hdr) images before the spatial normalisation stage. Could you tell me how to use '*.mat' files during the spatial normalisation? What should I pay attention to when I do this? Thanks a lot for your help. Ning Ma ----------------------------------------- Functional Imaging Lab Maryland Psychiatric Research Center University of Maryland, Baltimore On Thu, 18 Jun 1998, John Ashburner wrote: > Date: Wed, 17 Jun 1998 17:55:09 +0100 > From: John Ashburner <[log in to unmask]> > To: [log in to unmask], [log in to unmask] > Subject: realigning PET images > > Personally, if using SPM96, I would realign everything to the first image, > and create a mean realigned image. This would be followed by a second pass > where all the original images are aligned to this mean. This could in theory > be repeated many times, but I suspect that once is probably enough. > > SPM98 (SPM99?) will automatically use this two pass approach for PET images. > > Regards, > -John > > > A quick question about realigning PET images. what is the best technique? > > in the past i have selected 'all' scans and realigned in no particular > > order. i.e., the first scan selected for realignment was the first listed > > alphabetically. is it better to produce a mean image and then realign to > > that, or is there a specific order in which i should select scans? > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%