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
[EMAIL PROTECTED]
AG Kreiter / FB 2
Institut fuer Hirnforschung III
Abteilung Theoretische Neurobiologie
Universitaet Bremen
Biogarten
Hochschulring 16a
Postfach 33 04 40
28359 Bremen
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