When you use --regmethod volume, it assumes that the label coordinates
are in native anatomical space and then applies the mni305 registration
(talairach.xfm). In this case, your source subject is fsaverage so the
native space is assumed to be mni305 space (and talairach.xfm is the
identity). So if you don't start with mni305, the the output surely
won't be right. Second, when you use --regmethod volume, any surface
information will be lost (or inappropriate), which is probably why you
are seeing such chaos on the surface. I think by far the best solution
is to use --regmethod surface. Talairach is so inaccurate that 0-4mm of
misalignment is meaningless.
On 7/25/16 9:23 AM, Agoston Mihalik wrote:
Hi Freesurfer Developers,
I would like to ask for your expertise in the following problem I
encountered:
I want to create subject specific labels based on a label I created in
fsaverage. The transformation needs to be based on Talairach
intermediate registration, since my label was drawn based on Talairach
coordinates.
I ran the following command:
mri_label2label --srclabel test.label --srcsubject fsaverage
--trglabel lh.test2.label --trgsubject
subj222 --regmethod volume
The problem is that the output label is scattered and all around the
place when I look at it in tksurfer - see the image attached
(lh.regmethod_volume.tif).
When I did the registration based on surface, it worked fine (see the
image also attached - lh.regmethod_volume.tif), however, it resulted
in 0-4 mm misalignment when I looked at the Talairach coordinates of
the label borders. I guess it is due to the surface registration that
optimises the surfaces to be aligned, not the Talairach coordinates.
Please find some information attached in case it is any help – content
of files, output etc.
Here is my freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
Your help would be really appreciated.
Thanks and best,
Agoston
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