Dear Experts,
after ages of monkey scanning, we recently also included human subjects in our study. I would like to use freesurfer for surface reconstruction, mainly as "canvas" for the display of activation maps. While functional scans seem to be reasonable, the anatomicals taken on our Siemens Allegra (3T) with the default Siemens head coil are not well reconstructed by freesurfer (pial surface is both under- and over-inclusive, white matter in temporal pole is mis-classified as gray). Just in case it matters, test reconstructions were performed using the 64 bit centos_4 FreeSurfer 4.0.2 build on SuSUE 10.1 64 bit (and no errors in from the recon-all -autorecon1 and -autorecon2 stages). I assume that this is a driver's error on my part, as switching to the sequence parameters given on http:// www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min3T.html improves the quality of the reconstruction considerably. (Even though with our sequence we can actually set the FFT scaling factor.) Now I would be happy to know whether these protocol parametrs are still the recommended set for anatomical scans on an Allegra (using only standard "off-site" Siemens sequences)? I would also be grateful for anybodies input on the matter of "optimising" the raw data for the surface reconstruction, so manual interventions can be minimised.