Bruce,
thanks for the quick response. I have to bug you one more time, I have attached a screenshot of the wm volume,  would you correct the voxels classified as csf (on the top left corner) which, on the brainmask volume, appear as graymatter, or should I altogether stop worrying about gray matter structures misclassified as csf?
thanks a lot,
Binyam

Binyam Nardos
Cognitive Rehabilitation Research Group
Washington University School of Medicine Box # 8505
4444 Forest Park Blvd
St. Louis, MO 63108
Office: (314) 454-7795
Fax: (314) 286-1601



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-----Original Message-----
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]
Sent: Wed 3/21/2007 4:35 PM
To: Binyam Nardos
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] gray matter misclassified as csf

Hi Binyam,

don't worry about the subcortical regions in the wm.mgz (they were actually
classified as white matter, but it won't matter)

Bruce


On Wed, 21 Mar 2007, Binyam
Nardos wrote:

> Dear Freesurfers,
> after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes?
> appreciate any help,
>
> Binyam
>
> Binyam Nardos
> Cognitive Rehabilitation Research Group
> Washington University School of Medicine Box # 8505
> 4444 Forest Park Blvd
> St. Louis, MO 63108
> Office: (314) 454-7795
> Fax: (314) 286-1601
>
>
>
> The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.
>
>