If you want a simple brain mask, you can use brainmask.mgz. If you want to create a mask for a particular anatomical ROI, then you can use mri_binarize with --match. You can get a list of indicies from $FREESURFER_HOME/FreeSurferColorLUT.txt. I'm not sure what you are asking in terms of your selxavg3 question.
doug
On 4/7/12 1:04 PM, tomer@nmr.mgh.harvard.edu wrote:
Hi Bruce,
I seem to be missing something, sorry. How would I define this range? Also, how can I combine this mask with the functional results (obtained by running 'selxavg3-sess -s sj -analysis X.lh ...)? What I'll need eventually is a mask constrained both by anatomical and functional considerations (preferably with automatic anatomical segmentation as achieved by funcroi).
Thanks again, Tomer
Hi Tomer
don't use match - that would be for specific values. Instead specify a range via:
mri_binarize --min 1 --max 256 --i aparc+aseg.mgz --o aparc+aseg.mask.mgz
cheers Bruce
On Sat, 7 Apr 2012, tomer@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Thanks for the quick response. I got lost with the mri_binarize step, could you please explain to me how to find the value for the '--match' for different structures related to the aparc+aseg.mgz file?
Many thanks, Tomer
Hi Tomer
if you binarize the aparc+aseg.mgz with mri_binarize that should be pretty close. Do you need it in the functional geometry? If so, you can use mri_vol2vol to convert it (with a register.dat created by bbregister)
cheers Bruce
On Sat, 7 Apr 2012, Tomer Livne wrote:
Hi, I'll appreciate some help with the following issue. I need to define an ROI in a whole brain volume to be used as a mask in PyMVPA. That means having a whole brain .nii file with '1' within the ROI and '0' in every other voxel. Is there a way to define a functional ROI in a whole brain volume, in a similar way to what I get when running funcroi with an annotation from aparc for a specific hemi? Or alternatively, is there a way to convert the aparc based ROI for a single hemi surface into a whole brain volume?
Best, Tomer
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