Hi there:

Just to chime in a bit from a well-scarred SPM user who has had this issue many times, I'd add another tidbit to Kevin and Luca's great advice:

1. Pull a copy of the template you're interested in, so you can have it up next to your image in 'Display" while you're working. Or have 2 copies of SPM open...

2. SPM12 if its an option for you has a nice revision of the 'set origin' and 'reorient' functions in 'Display' that is more user-friendly and a little bit quicker (IME) than SPM8.

Good luck!
Nina


On Sun, 27 Nov 2016, Kevin London (SCHN) wrote:

> 
> Hi Bianca,
> 
>  
> 
> I agree with Luca that your problem is most likely not setting the origin of your scans to the AC (because this was the same problem that I had!). As well as checking
> the origin of the scans, I’d check the origin of your custom template as well. Use “Display” to do this as Luca has suggested. I did 30 scans manually and you get
> quite fast at it.
> 
>  
> 
> Also, the default bounding box dimensions in SPM8 seemed to chop off my scans through the temporal pole so I changed my bounding box to…
> 
> -90          -126       -72
> 
> 91           91           109
> 
>  
> 
> … and this seemed to work with my pediatric PET scans.
> 
>  
> 
> Regards,
> 
> Kevin
> 
>  
> 
>  
> 
> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of PRESOTTO LUCA
> Sent: Sunday, 27 November 2016 22:53
> To: [log in to unmask]
> Subject: Re: [SPM] Registration to an house PET template SPM8
> 
>  
> 
> Yes, the image you need to normalize must have an origin so that there quite close to the template, to begin with.
> As a convention, the origin is set in the anterior commisture. (But it doesn't really matter to normalize, as long as it's the same in both images... But then the
> template wouldn't be in mni space.)
> 
> So,anyway...
> Start checking the orientation of your template using the display function.
> Then put all the images in the same orientation, using the reorient function.(just write if you don't know how to do it)
> If you have few scans I recommend doing this manually, so that you can check quite well how's everything.
> If you have a lot, I have a script that first sets the origin to the centre of mass of the image, than uses the coreg to coregister the image to the template, so that
> initial alimenting is the best.
> 
> Have a nice Sunday,
> Luca
> 
> Da: De Blasi, Bianca
> Inviato: domenica 27 novembre, 11:08
> Oggetto: Re: [SPM] Registration to an house PET template SPM8
> A: PRESOTTO LUCA, SPM (Statistical Parametric Mapping)
> 
> Dear Luca,
> 
> thank you for your reply. I get a blank output (black image when I open the image in CheckReg with the template image).
> 
> Do the source images need to have the same origin as the template? How can I check this and reset the centre, in case it is not correct?
> 
> Thank you,
> 
> Kind regards,
> 
> Bianca
> 
> From: PRESOTTO LUCA <[log in to unmask]>
> Sent: 27 November 2016 09:56:17
> To: De Blasi, Bianca; SPM (Statistical Parametric Mapping)
> Subject: Re: [SPM] Registration to an house PET template SPM8
> 
>  
> 
> Dear Bianca,
> I think that you should give us an example of what you mean by "do not work". Do you get a blank output? Or weird deformations?
> 
> My first bet, anyway, would be to check if all the images have their origin correctly set.
> 
> Luca
> 
> Da: Bianca De Blasi
> Inviato: venerdì 25 novembre, 18:13
> Oggetto: [SPM] Registration to an house PET template SPM8
> A: SPM (Statistical Parametric Mapping)
> 
> Dear experts, I am trying to register a set of paediatric PET images to an in house paediatric PET template using Normalise (Est&write) module of SPM8. I select one of
> the PET images as the 'Source Image' and 'Image to write' and the in house PET template as the 'Template image' and leave all the images as default (but the bounding
> box and voxel size, which are set to the one of the template). The registration does not work for any of the PET images and the resulting registered images are very
> far off from the target template. Could you please suggest which option I can change to make the registration work? Thank you very much in advance, Kind regards,
> Bianca
> 
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