Dear Keith,

John Ashburner will be able to give you a much more comprehensive answer, but I thought I'd add my bit. Firstly, did you use one of the spm template brains as your template? Those brains include the skull, and so it might be that the normalisation would not work particularly well if you are trying to register skull-stripped images. I believe (you could check in spm_help) that the normalisation initially uses both the brain and skull in the early stages, and so if it encounters images without skull this may cause problems. As a more general point, John has provided a nifty way using the imcalc button to remove traces of skull from segmented images. From the render button select the grey and white matter images and choose to save the extracted brain. Then from imcalc select the grey matter image and then the extracted brain (which begins brain*) and evaluate the function i1.*i2

It is of course possible that one or more of your images did not register and segment, which can have a major effect on your findings, although it sounds like you checked this.

When you set up the SPM analysis it asks you to select the grey matter threshold (default 0.8). This is used to identify those voxels which have a high probability of being grey matter, and therefore should be included in your analysis. It first of all calculates the overall mean intensity value and then removes all voxels that fall below 1/8 of that value (I'm not absolutely sure about this, but someone will correct me if it's wrong), assuming they represent nonbrain tissue. It then recalculates the mean of the remaining voxels, and then only includes in the analysis those voxels that survive the threshold you specified. You may want to look at the mask.img file in the results directory to check it. Although you can't "limit" the search space (that I know of), you could alter the threshold to make the criteria for voxel inclusion more stringent.

You don't say how far the differences are outside the brain, and whether this is visual on overlay maps, or in terms of xyz coordinates. One mistake I made in the past was in specifying header information. If you give the wrong voxel size, it is possible that the Talairach coordinates will be completely wrong.

There isn't a way of specifying "plugs" of tissue types. The segmentation already incorporates prior knowledge of the likelihood of any particular voxel being grey matter (for example), and this is used to weight the segmentation. If you are finding some sort of smearing during segmentation, you could try changing the voxel size of the written out normalised images (via the defaults button), as you may find that a 1mm cubic voxel size gives you a cleaner segmentation.

Sorry my bit was so long,

Xavier


  

>Hello all -
>
>I am running a voxel-based morphompetry analysis. After skull stripping the
>brains i ran them through the spatial normalization, initially with all the
>set defaults. Subsequent to normailzation the images were semgented within
>spm into their respective gray, white, and csf compartments then smoothed.
>When i ran the acutal analysis, spm showed significant voxel intensity
>differences outside of the head. After inspecting each of the normalized
>brains for any outlying tissue that may have been left after the skull
>stripping and not finding any, i attempted a strictly linear normalization.
>The results after running the analysis was the same with the same voxels
>lying outside the head. Additionally any tweaking of the non-linear
>funcions, either in the amount of functions used or amount of iterations,
>yielded little change in the overall result. Has anyone else seen this? If
>so, how did you correct for it? I am wondering if there is a way to limit
>the search space that spm "looks" for significance between the voxels, that
>i could exclude the area outside of the head.
>
>Also, is there a way to specify "plugs" of brain tissue to classify voxel
>intenstiy ranges for gray, white and csf prior to running the segmentation?
>The segmentation result i get is generally very good with only some
>"smearing" of gray and white in the basal ganglia and cerebellum, that i
>feel could be alleviated if prior knowledge of the intesities of those areas
>were incorported ahead of time.
>
>thanks in advance for any input.... keith
>
>-------------------------------------------------
>Keith Harenski
>Neurobiology Lab
>WPIC Rm#986
>


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