Hi Sebastian,
we put together some Allegra-specific postprocessing tools that helped for
Mike Chee (ccd). Maybe Mike can give you the benefit of his experience?
cheers,
Bruce
On Tue, 22 Jan 2008, Sebastian Moeller wrote:
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.
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
