Sounds like you should look at the wmparc which includes the cortical labels as well as white matter labels based on proximity to the nearest cortical label. If this works for you, you can create a mask with

mri_binarize --i wmparc.mgz --match 2030 --match 4030 --o rh.stg.mask.mgz

2030 and 4030 are the codes for cortical and nearest-wm for the right STG as found in $FREESURFER_HOME/FreeSurferColorLUT.txt

doug

Anil Roy wrote:

Hello All,

I want to create a binary mask volume for stg and tried the following command

# mri_label2vol --label trial_labels/rh.superiortemporal.label --temp /mnt/win/MRI_data/Trial_Runs/Freesurfer/1195/mri/brainmask.mgz --o testmask.mgz

The label was created using mri_annotation2label

When I opened up this label in tkmedit, I could see that the cortical regions of STG are in white and everything else is in black. My questions is if it is possible to fill in the regions within this label: in other words if I can also have the white matter that the label encompasses included in the mask.

Also, is there a different method that is normally used for creating binary masks?

Thanks,

Anil.
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