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?
>
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