sure, you can do it easily enough in matlab:

[v,M,mr] = load_mgh('aseg.mgz') ;

gm = find(v == 3 | v == 42 | (v >9 & v <=13) | v == 17 | v==18 | (v >48 & v <= 54) | v == 47 | v== 8|v==26|v==58|v==80|v==30|v==62);

wm = find(v == 2 | v == 41 | v == 7 | v == 46 | v == 16 | v == 60 | v== 77|v==85|v==28) ; csf = find(v == 4 | v == 24 | v == 14 | v==15 | v == 72 | v == 5 | v == 43 | v == 44|v==63|v==31); v(gm) = 150 ; v(csf) = 10 ; v(wm) = 250 ; save_mgh(v, 'aseg.trinary.mgz', M, mr) ;

this script will convert an aseg into a 3-valued output (10=csf, 150=gm, 250=wm)

cheers Bruce

On Wed, 27 Feb 2013, Azeez Adebimpe wrote:

Hi Bruce,

Thank for your response. I am trying to separate white matter, gray matter and csf from aseg.mgz base on the intensity values of subcortical tissues. My aim is to have  GM, WM and CSF of both hemispheres not only left hemisphere, is it possible?

Azeez

.....

Hi Azeez

no, both hemispheres should be labeled by default. Are you sure it's not just the colors that are confusing you? The left hemi WM is shown in white by default, but if you mouse over it in freeview or tkmedit it should show the label Left-Cerebral-White-Matter.

cheers Bruce

On Tue, 26 Feb 2013, Azeez Adebimpe wrote:

Hi freesurfer experts, The output of  the segmentation, aseg.mgz only display right hemisphere. I used option -all in the segmentation. How can I make the both hemispheres visible or is there any specific option to choose  for segmentation to make both hemispheres visible?

Thank you/

Azeez Adebimpe

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