Hi Nick, hi All,
On 22. Feb 2006, at 19:39 Uhr, Nick Schmansky wrote:
In the freesurfer dev releases post 2006-18-01, there is a -noaseg flag
in recon-all. It will skip the auto-segmentation step, and not include
aseg.mgz in any subsequent processing (eg. wm seg and filling). The
flag is intended for usage with baby brains and non-human primates, as
these brains cannot be auto-segmented with the default atlas (which is
based on 40 adult normals).
I still run the dev20051003 version, is everything else compatible?
Anyway I used the -nofill directive for recon-all autorecon2-wm, after
running mri_fill manually, supplying the required cc and pons
coordinates, but specifying -noaseg sure beats my "do it by hand"
approach, by far. Thanks for the impressive automatization work.
Ahoi & Thanks
Sebastian
On Wed, 2006-02-22 at 18:19 +0100, Sebastian Moeller wrote:
Dear all,
at the moment I am struggling with flattening monkey anatomical scans.
Specifically I manually got to the point where I get a wm.mgz and now
I
want to inflate it. My instructions refer to using csurf, which does
not like my mgz volumes and is deprecated IIRC, the alternative is
hooking my data into the recon-all pipe-line. But that fails as I do
not have any aseg.mgz (does the segmentation work for monkeys?). So
any
advice on how to proceed with the processing?
Ahoi & Thanks
Sebastian
--
Sebastian Moeller
Tel.: 04 21 - 2 18 - 78 38 oder 96 91
Fax.: 04 21 - 2 18 - 90 04
GSM: 01 62 - 3 25 45 59
[EMAIL PROTECTED]
AG Kreiter / FB 2
Institut fuer Hirnforschung III
Abteilung Theoretische Neurobiologie
Universitaet Bremen
Biogarten
Hochschulring 16a
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28359 Bremen
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