Hi all,
I'm attempting to use FreeSurfer 5.1 (version block below) to process some older T1 scans collected on a 1.5T magnet with a native voxel size of 0.9375x0.9375x1.5mm. Overall, FreeSurfer seems to deal with these scans just fine (resampling to 1 mm isotropic, etc.), but I'm a little concerned about the results of the built-in image normalization.
The potential issue is illustrated in an image that I've posted to http://imgur.com/NiEVQ. The isolated plot to the right shows the intensity histogram that we've observed for more recent 3T T1 scans, with an obvious WM peak at 110 and a GM peak around 65. Meanwhile, each of the six plots to the left is the intensity histogram for one of our 1.5T scans. Although they are internally consistent (with the upper-leftmost example being something of an outlier), the GM peak is much closer to the WM peak, with a mode around 85.
I'm wondering whether this reduced GM/WM separation is likely to influence the tissue segmentation process, and if so how I might best remedy the situation. At a guess, mri_normalize or mri_ca_normalize seem like useful functions, but I haven't found the documentation for either to be of much help. Any assistance or advice would be greatly appreciated! Thanks,
Dave Warren