Hi Michael,
On Jan 22, 2008, at 4:18 PM, Michael Chee wrote:
Hi Sebastian and Bruce,
I'll respond by the end of the week as I have some things to tend to presently.
Cool, thanks a lot and no hurry (no(t much) time this week either for testing/acquiring new anatomical scans myself).
ahoi & thanks Sebastian
Mike
From: Sebastian Moeller sebastian.moeller@lur.rwth-aachen.de Date: Tue, 22 Jan 2008 15:10:15 +0100 To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: Mailing Freesurfer List freesurfer@nmr.mgh.harvard.edu, Andre van der Kouwe andre@nmr.mgh.harvard.edu, Mike Chee mchee@pacific.net.sg Subject: Re: [Freesurfer] recommended scan parameters
Hi Bruce,
thanks for your quick response.
On Jan 22, 2008, at 3:06 PM, Bruce Fischl wrote:
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?
That would be marvellous. Thanks in advance.
ahoi Sebastian
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.
-- Sebastian Moeller
Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 moeller@brain.uni-bremen.de
AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen