Kazu,
This is for a non-human primate, right? If so, you will need to
manually define seed points for the corpus callosum and pons. To do so,
open the white matter volume in tkmedit:
tkmedit <subjid> wm.mgz
and using the cursor, identify the 'volume index' of the point where you
think the corpus callosum is located and make a note of it (for
instance, in an example subject 'bert', its around 128 117 123). Also
make a note of where the pons is located.
Then, restart recon-all from mri_fill, passing those coordinates, for
example:
recon-all -s bert -autorecon2-wm -noaseg \
-cc-crs 128 117 123 \
-pons-crs 128 154 108
Nick
ps, i've posted this to the list as others may have a better suggestion.
On Mon, 2007-01-22 at 12:55 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
> Hi Nick,
>
> Thank you so much. It worked.
> Now I got an error message at 'mri_fill'.
>
> The message says:
> mri_fill: could not find corpus callosum
> INFO: Modifying dst c_(r,a,s), using the transform dst
> find_cutting_plane:seed point not in structure! Searching neighborhood...
> recon-all exited with ERRORS at Mon Jan 22 10:57:43 EST 2007
>
> Is this error due to -noaseg flag? What should I do next?
>
> Kazu
> -----Original Message-----
> From: Nick Schmansky [mailto:[EMAIL PROTECTED]
> Sent: Sun 1/21/2007 6:38 PM
> To: Tanji, Kazuyo (NIH/NIMH) [F]
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] -noaseg
>
> Kazu,
>
> It looks like the -noaseg option does make use of norm.mgz (a change
> that seems to have occurred since the option was created and tested).
>
> As a work-around, you should be able to do this:
>
> ln -s brainmask.mgz norm.mgz
>
> and then run the -autorecon2 -noaseg flags. brainmask.mgz is a close
> enough stand-in for norm.mgz.
>
> Nick
>
>
> On Sun, 2007-01-21 at 17:45 -0500, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
> > Hi,
> >
> > I have a question on how to use -noaseg option.
> >
> > I tried a script: recon-all -autorecon2 -noaseg -subjid xxx.
> >
> > This seems to skip several steps of autorecon2 and start from
> > 'mri_normalize' . This results in an error because norm.mgz is not
> > existing.
> >
> > Could you suggest better ways to use -noaseg?
> >
> > Thanks,
> > Kazu
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
>
>
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