Hi Doug,

Thanks for your reply.

The mask created is used to register with the normalized functional data and to define the roi, so could I run the following command?

 

tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg ./register.dat/

 

and the func.nii has been normalized (sub.nii) to the MNI space.

 

The .w file I download from http://ltl.tkk.fi/wiki/Atlas, indicates the maximum probability map.

 

Best wishes,

 

Meng

 

 

 

 

 

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