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
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