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Thank you John, for the guidance. Actually I was running the code with the user interface and still it was happening; so I m not sure if it happens because of some other changes or not. But anyway this problem is solved now as I put the values as described by you and it works. However the results of co-registration are really bad (as inspected visually). I m working on the mice data and also using the spmmouse plugin to make it compatible with the mice data. I also did the manual registration first and tried to bring the two images as close as possible and then run the automatic co-registration of spm, but still the co-registration results are really bad in terms of that it cut part of one image while co-registering. Thus in the end we have co-registered images, but part of them is cut down... is there any solution or any suggestion to achieve better co-registration ?
Thanks a lot
best regards,
Qasim


Qasim Bukhari

Research Assistant and Doctoral Candidate

Institute for Biomedical Engineering

ETH and University Zurich

Wolfgang-Pauli-Strasse 27, HIT E22

webpage: http://www.micro.biol.ethz.ch/people/sybukhar/index




> Date: Thu, 2 Feb 2012 17:04:55 +0000
> From: [log in to unmask]
> Subject: Re: [SPM] error while doing co-registration !!
> To: [log in to unmask]
>
> The setting for the histogram smoothing should have two values, which
> default to [7 7]. I'm not sure where the scalar value of 0.56 is
> coming from. The problem is arising because the coreg routine expects
> fwhm to contain the two values, whereas it appears to only contain
> one. As far as I can tell, this should not happen if you run the code
> via the user interface.
>
> Best regards,
> -John
>
> On 2 February 2012 12:40, Qasim Bukhari <[log in to unmask]> wrote:
> > Dear all,
> > I m trying to co-register a few images, but constantly getting the error.
> >
> > Error running job: Attempted to access fwhm(2); index out of bounds because numel(fwhm)=1.
> > In file "C:\Users\BUKHARI\Desktop\PhD_Markus_Rudin\resting state\spm5\spm_coreg.m" (v1007), function "optfun" at line 160.
> > In file "C:\Users\BUKHARI\Desktop\PhD_Markus_Rudin\resting state\spm5\spm_coreg.m" (v1007), function "spm_coreg" at line 82.
> > In file "C:\Users\BUKHARI\Desktop\PhD_Markus_Rudin\resting state\spm5\spm_powell.m" (v691), function "spm_powell" at line 27.
> > In file "C:\Users\BUKHARI\Desktop\PhD_Markus_Rudin\resting state\spm5\spm_coreg.m" (v1007), function "spm_coreg" at line 134.
> > In file "C:\Users\BUKHARI\Desktop\PhD_Markus_Rudin\resting state\spm5\spm_config_coreg.m" (v1032), function "estimate" at line 281.
> >
> > Just a simple search of the error over the internet showed me that this question was asked by somebody else before as well on this group; but nobody had proposed its solution.
> > For the histogram smoothing I m using the value 0.56, the default, and also for the rest of other parameters I m using default values.
> >
> > Can somebody please help ??
> > Thanks a lot and best regards,
> > Qasim