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:nicks@nmr.mgh.harvard.edu] 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

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