On 04/25/2013 10:13 AM, limengsecret wrote:

Dear FreeSurfers, I want to convert cortical labels to volumetric masks, and I run the following commands:

1. /tkregister2 –mov sub/mri/rawavg.mgz –noedit –s sub –regheader –reg

./register.dat/ 2. /mri_label2vol –label ./lh.entorhinal.label –temp sub/mri/rawavg.mgz –subject sub –hemi lh –o sub_lh_entorhinal.nii.gz –proj frac 0 1 .1 –fillthresh .3 –reg ../mri/register.dat/ if I do not run the recon-all command, could I change the rawavg.mgz to sub.nii (original data)?

What is sub.nii?

The second problem is that when I convert the annotation file to volumetric mask, whether I should convert the file to labels using mri_annotation2label first, then run the commands as decribed above, or there is a way that could convert the annotation file to volumetric mask directly?

You can use the same label2vol command above but spec --annot instead of --label

The last problem is that how to convert the .curv file and .w file to volumetic mask?

mri_surf2vol should work for the curv file. Why do you have a .w file?

BTW, for our standard annotations (aparc and aparc.a2009s) you will probably be happier with the results if you use mri_label2vol with --seg aparc+aseg.mgz or --seg aparc.a2009s+aseg.mgz. Otherwise, there are some holes that are created if you use the surface labels.

doug

Any help will be very appreciated. Best wishes, Meng

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