Hi Freesurfer experts,
I asked this question previously, but I found it problematic when displayed
in your mailist. I'm sorry that the question still not solved and I feel
sorry to trouble you again.
In your sphere registration in freesurfer, the procedure is like: creating
the template.tif by mris_make_template. The template you use in
Freesurferis created by iterative registration of 40 subjects,
according to
"High-resolution inter-subject averaging and a coordinate system for the
cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M.,
(1999). Human Brain Mapping, 8:272-284(1999)".
So, after the template generation process, you will get a .tif file which
include the necessary infomation (like the means and variances of curv, sul
from the aligned spheres). But,do you have the other information of this
final template, such as the sphere representation, folded surface
representation of this template? I know that under
*/subjects/fsaverage/surf, there are some surface representations of the
average of the 40 subjects, but to my knowledge, they are just used for
visulazation and are not the surface representation of the template.tif you
used, am I right?
2, subjects' sphere registration to the template sphere
In this process, we can get the deformed subjects spheres( *.reg ), which
have a one-to-one correspondance to the original subject surfaces. Except
the .reg sphere with the cuvature information, do you have any other form of
representation of the deformed sphere? You know that there are other kinds
of surface mapping methods, like Miller's Large Defformation deffeomrphic
surface mapping, they just do surface mapping using the folded surfaces.
After surface mapping, they will get the deformed folded surface which would
be aligned with the template folded surface. With the deformed subject and
template folded surfaces, they can tell directly which sulcus or gyrus is
aligned well. So, for your mapping, when I get the deformed sphere, do you
have any command or method to put the sphere back to the folded surface so I
can see the suci and gyri directly? If you also have the surface
representation of the template, then i can superimpose them to see how good
the alignment is.
If you think I didn't state this problem clearly, please refer to an example
in the following:
I found one reference using your sphere registration method. "Simpli˙˙ed
Intersubject Averaging on the Cortical Surface Using SUMA"Brenna D. Argall,
Ziad S. Saad,and Michael S. Beauchamp"Human Brain Mapping 27:14 ˙˙27(2006)"
mris_register [Fischl et al., 1999b] routine, each individual subject˙˙s
surface was registered to the FreeSurfer average7 template prior to node
number standardization. Standardization and averaging were then performed on
the surfaces as described above" (using SUMA FYI).
---- From this part, I assume that all the deformed surfaces are in
spherical representation.
Then in the result part, in section "Intersubject Averaging of Functional
Data: Different Surface Methods", they mentioned they " in order to compare
the AC˙˙PC method to these more complex algorithms, the FreeSurfer program
mris_register [used in Fischl et al., 1999b] was used to morph the cortical
surface models to a prede˙˙ned template, and these morphed surface models
were then used to create a morphed surface average."
In Fig7C ˙˙Average surface created by averaging the same 28 subjects using
mris_register standardization. You can see that they show the average
surface in a folded surface representation, not a sphere.
Could you give me a hint that how they do this since you only have a sphere
representation of the aligned surface?