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SPM  February 2012

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Subject:

Re: error while doing co-registration !!

From:

John Ashburner <[log in to unmask]>

Reply-To:

John Ashburner <[log in to unmask]>

Date:

Fri, 3 Feb 2012 12:46:38 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (96 lines)

I don't have a lot of experience of working with mouse brains, but
make sure that the values in the "Separation" field of the GUI are
sufficiently small.  By default, the registration is done by sampling
the data roughly every 4mm to quickly obtain a coarse estimate, and
then it continues by sampling roughly every 2mm to get a more refined
estimate.  For mouse brains, you may need to change these values to
something much smaller (eg about 4x and 2x your voxel sizes).

Your tweaking of the initial orientations was a good idea as it should
provide better initial starting estimates.

I'm not sure what you mean when you say that the registration cut part
of one image.  Is it possible that this part was not included within
the original field of view of the image?

Best regards,
-John


On 3 February 2012 10:59, Engr. Bukhari <[log in to unmask]> wrote:
> 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

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