Dear Marris,

Well, I'm not really sure what this screenshot shows (the segmented grey matter image?), and how it was visualized. It looks like a binary image with zeros and ones, but maybe this is just due to some display settings, coding anything non-zero as white. See attachements for 1) the raw structure and the c1 grey matter image obtained with "Segment" in SPM12, visualized within SPM, and 2) the grey matter tissue probability map as provided with SPM and the wc1 normalized grey matter image as obtained with the same routine.

The output seems to be reasonable. It is not perfect, e.g. some white matter is classified as GM (see raw&c1_WML). This is not surprising though, as the raw image clearly shows some intensity changes, pointing to periventricular white matter lesions (and/or artefacts). It's not a matter of algorithm (SPM12 Segment vs. SPM8 vs. VBM8), but would require a special preprocessing pipeline to avoid misclassifications (e.g. some additional tissue probabiliy maps coding regions where WML are likely to occur).

What bothers me a little is the contrast of the raw image. When looking at e.g. the topmost slices or at some of the sulci there is hardly any contrast between grey matter and white matter. It would thus be impossible to properly segment the image manually. The segmentation algorithm results in a reasonable image, but this is also because it is forced to classify things as grey matter due to spatial constraints. Thus it would be interesting to see the true raw image. I have doubts the current one is really the true one. When displaying it with a different intensity mapping it becomes evident that voxels around the head are coded as zero = there is no noise, which is very surprising given the usual low-intensity noise. Based on the sharp edges some correction must have been performed on that image. And then the question arises, which type of correction was performed and how did the raw data look like before that step? It might just have been some bias correction, but it might also have been prospective motion corrections like PROMO.

For illustrative purpose I've also attached an unaltered T1 image screenshot affected by motion (motion artefacts can be much worse). Posteriorly, at the enlarged sulci, it's (almost) impossible to identify the cortical sheet, it looks like CSF -> brain tissue, not CSF -> GM -> WM. Anteriorly, quite some smearing is evident. Maybe this was also the case in your file, after some motion correction the blurring might have been reduced, but the contrast might still be quite low. This is just guessing of course. It would be necessary to see some of the other images to get an impression whether this is due to the scanner/sequence settings or whether it's a problem in particular volumes. The contrast might have been low due to the settings, but it might also have been due to motion or an artefact introduced during the correction step. 

Best

Helmut