Hi Prapti,

Basically, you just need to have a label file that you can turn into a lh.your_annot_name.annot (assuming your actual ROI is in the right hemisphere), so that mri_label2annot runs properly.

The easiest thing to do would be to rename any old label you have in your subject's label directory to lh.dummy.label, and then create an annotation from that label with mri_label2annot. Then run mris_aparc2aseg as you tried to do before, which will create a volume that has 0's everywhere except in the area where your actual and dummy labels were projected. Figure out the voxel values for the ROI you want (using Freeview or tkmedit), and then run:

mri_binarize --i your_annot_name+aseg.mgz --match <that voxel value> --o you_roi_name.mgz

Which will have 1s where your ROI is and 0s everywhere else.

Best, Mike

-------Original Message-------

Hi Doug, Thanks for the reply. I am sorry, I am a bit confused about what you mean by creating a dummy label. I am also not sure at which step I need to do this.

As I understand it, I use mri_label2annot to transform my label into a annotation file and this will be separate for the two hemispheres. Do I then edit these files ? where exactly do I use mri_binarize?

Thanks,

Prapti

-----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Friday, 17 September 2010 12:44 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues

Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The

easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere.

doug

Prapti Gautam wrote:

Hi Doug,

Thanks for the reply. I have tried using the method you've suggested, however, I'm stuck because mri_label2annot which I use to turn my

label

into a annot file only works in one hemisphere while mri_aparc2aseg works for the whole brain. Do you know a work around for this?

Can I merge the annot files created from each hemisphere so that I can pass it to mri_aparc2aseg?

Thanks,

Prapti