For aparc+aseg, the cortex does not take values 3 and 42. Instead, the cortex is divided into regions of interest that range from 1000 to 1999 (left hemi) or 2000-2999 (right).
doug
ps. Please post questions to the list and not to us personally. Thanks!

On 4/2/12 5:15 AM, lorenzo pasquini wrote:
Hi Douglas,

thank you for replying. Actually I was wrong, there is no ID problem for the right cerebral cortex: the ID is 42 in both the aseg.stats file and in the FreesurferColorLUT table. But the problem in building the masks persists. I am able to build mask of several brain parts (amygdala, crebral white matter, hippocampi) but not of the cerebral cortexes. The command lines I use are:

mri_binarize --i aparc+aseg.mgz --min 2.5 --max 3.5 --o leftcc.nii
mri_binarize --i aparc+aseg.mgz --min 41.5 --max 42.5 --o rightcc.nii

I am using freesurfer version 4.3.0_64bit.
Thank you again and kind regards,

Lorenzo

Da: Douglas N Greve <greve@nmr.mgh.harvard.edu>
A: freesurfer@nmr.mgh.harvard.edu
Inviato: Venerdì 30 Marzo 2012 19:07
Oggetto: Re: [Freesurfer] problem in building cortex mask

what is your command line?

On 03/30/2012 12:00 PM, lorenzo pasquini wrote:
> Dear freesurfers,
>
> I have a problem in creating  masks of the left and right cerebral
> cortexes. The message "found 0 values in range" is displayed and an
> empty mask is created. This is surprising as I am able to build masks
> of the right and left hippocampi and entorhinal cortexes using the
> same command without any problems. Further the satistic file
> aseg.stats indicates me a huge amount of voxels in the cerebral
> cortexes. I am using the segmentation ID  3 for the left cerebral
> corex and 42 or 53 for the right cerebral cortex. I am surprised as
> well to find two different IDs for the same region, 42 comes from the
> aseg.stats file, 53 comes from the FreesurferColorLUT table. Wich ID
> is the right oneto use?Why can I build  masks of hippocampal regions
> but not of the cerebral cortexes?
> Thank you very much and kind regards,
>
> Lorenzo Pasquini
>
>
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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