[Freesurfer] R: R: Re: Mask from cortical parcellation

I mean anatomical.nii.gz with the same spatial features of the masks. Thanks,

Stefano

----Messaggio originale----

Da: stdp82@virgilio.it

Data: 4-set-2013 23.02

A: greve@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu

Ogg: [Freesurfer] R: Re: Mask from cortical parcellation

Thank you very much. A last help, please. How is the anatomical file that I can use to overlay the masks. I'm noting that masks are characterized by:data_type INT32dim1 256dim2 256dim3 256dim4 1datatype 8pixdim1 1.0000000000pixdim2 1.0000000000pixdim3 1.0000000000pixdim4 0.0109999999cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ Regards,

Stefano

----Messaggio originale---- Da: greve@nmr.mgh.harvard.edu Data: 4-set-2013 17.10 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Mask from cortical parcellation

you can use mri_binarize on aparc+aseg, eg, something like

mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1032 --o frontal.nii.gz

those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt That table has a lot of ROIs in it, and not all will be in the aparc+aseg. You'll be interested in the ones between 1000-1035 and 2000-2035

doug

On 09/04/2013 08:46 AM, stdp82@virgilio.it wrote:

Hi list,

I need to create a mask of frontal, parietal, temporal and occipital lobes in a subject by using cortical parcellation output.

Is it possible? Eventually, how can I transform these masks file to mii.gz (to import them in FSL analysis).

Thank you very much.

Regards,

Stefano

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