Dear Lucy,

Some ideas:

1. Brainstem is not defined properly in the AAL. You can check the Hammers and the LONI atlases, they include the brainstem at least. If you really want the pons, you may need to draw/define the region yourself.

2. I am not sure if I got your point clearly... but if what you want is to use the mean uptake value of the pons obtained from each corresponding image as the reference region for the normalization procedure, instead of the whole brain uptake as is done more frequently, then you can extract the values of the pons of each image using any software available (marsbars, FSL, or even SPM with 'spm_summarise(input_PET_image,image_with_the_pons,@mean)' ) and then use this vector of values (not 2x1 vector, it has to be one value for each corresponding image) as input in the user-defined option in the global normalization section.

Please let me know if this is not clear enough, and I can give you some extra help.

Best regards,

David Vállez

On Sat, Aug 22, 2015 at 3:21 AM, Lucy Haggstrom <[log in to unmask]> wrote:

Hi all,
I am very new to SPM am trying to intensity normalise two static PET images from the same patient (obtained weeks apart) to the pons. We cannot use global normalisation since the condition we are studying appears to be associated with changes in the global signal. We believe the pons and cerebellum to be relatively spared by the effect of the condition.

I have a number of questions:
1. How can I get the raw data for uptake in the pons? I have managed to use mars bar to extract data from the cerebellum using templates from AAL, but cannot find a pontine template.
2. Once I have the raw data, how can I scale each image to this? Do I do this before I set up the model (paired-t test) or is it part of the model? I have had a go at using imcalc to divide i1 by the raw value for the cerebellum (e.g. using the expression f = ‘i1./17000’) but this gives me an error message (undefined function or variable). I have also tried using the user-defined option in the factorial design specification, entering a 2x1 vector of raw data for the cerebellar uptake in the two scans, and no other normalisation steps. However when I do this i get an error in spm_est_smoothness (FWHM(~FWHM)=1).... I’m assuming this is error message is from something other than the normalisation step, but am not sure where.. I have warped both scans to a PET template and then smoothed them (FWHM 16), using implicit masking.

Any help would be greatly appreciated!

Thanks,
Lucy