Sebastian, I've attached a gzipped recon-all that has the -noseg flag. Do not copy over the recon-all in your 2005-10-03 release, as it's not fully compatible with that. Rather, I suggest opening the new recon-all in a text editor, and look for instances of the variable 'UseAseg', and the - noaseg flag, and I think you can modify your existing recon-all to do the same. There is no magic involved, the -noaseg flag just does what you were probably doing manually. Your 2005-10-03 release should work with the changes.
Nick On Wed, 2006-02-22 at 20:02 +0100, Sebastian Moeller wrote: > 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 > > > > > >
recon-all.gz
Description: GNU Zip compressed data
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