HI Courtney, please post to the list. Thanks! Get the codes from $FREESURFER_HOME/FreeSurferColorLUT.txt. Also, you can use multiple numbers to match all the ROIs you want at once (if that is what you want). Eg, --match 2 26 17

doug

On 04/22/2014 03:16 PM, Courtney Haswell wrote:

Thanks for the reply. I was able to make the hippocampus and amygdala masks easily, but was having some trouble for the other ones.

Looking in the "aparc.annot.ctab" file, I see that caudalanteriorcingulate is labeled 2 and rostralanteriorcingulate is 26. So then is this the correct way to get the ROI extracted: mri_binarize --i $SUBJDIR/aparc+aseg.mgz --o $ROIDIR/3_rostralACC.mgz --match 26 mri_binarize --i $SUBJDIR/aparc+aseg.mgz --o $ROIDIR/3_caudalACC.mgz --match 2

I also did the caudal ACC (that is in aparc.annot) the same way but that ROI covers all of the white matter in the right hemisphere so I think I did something wrong. mri_binarize --i $SUBJDIR/aparc+aseg.mgz --o $ROIDIR/3_caudalACC.mgz --match 2

mri_mask $SUBJDIR/aparc+aseg.mgz $ROIDIR/3_caudalACC.mgz $ROIDIR/acc_mask5.mgz

Thank you, Courtney

Use mri_binarize with the --match option to create a mask of the regions you want. Then use mri_mask applied to aparc+aseg to create a new volume with only the regions you want doug On 04/22/2014 09:06 AM, Courtney Haswell wrote:

...

Hi!

I want to view only certain segmented regions on one of our subject's brains. It seems like it should be simple but I am struggling to find the steps. I want to display only hippocampus, amygdala, medial orbitofrontal, lateral orbitofrontal, sulcus/gyri anterior cingulate, subcallosal gyrus, and rACC and cACC.

How do I extract these labels so that I can only show just these regions on the brain? I extracted stats for these areas, but want to visually show the locations.

Thank you, Courtney