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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