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. "Simplified 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)" You may see the attachment in : https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-May/010558.html
In "Spherical Morphing" section, They mentioned that " Using the 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 predefined 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?
Hi Jidan,
the atlas only exists in spherical coords. To represent a folded surface we either (1) map to an individual subject, or (2) use a volume transform such as tal and the vertex correspondence from the sphere.reg to find the average coordinate of a vertex. This is how we build the fsaverage and average7 surfaces (we know this is a hack, but it's easy and a good visualization tool).
You can use the mapping to paint the geometry of one subject onto another folded surface if you want to visualize the geometric mapping (e.g. the curv of one subject on the white surface of another).
cheers, Bruce
On Tue, 21 Jul 2009, Zhong Jidan wrote:
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. "Simpliÿÿed Intersubject Averaging on the Cortical Surface Using SUMA"Brenna D. Argall, Ziad S. Saad,and Michael S. Beauchamp"Human Brain Mapping 27:14 ÿÿ27(2006)" You may see the attachment in : https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-May/010558.html
In "Spherical Morphing" section, They mentioned that " Using the mris_register [Fischl et al., 1999b] routine, each individual subjectÿÿs 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 ACÿÿPC 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 predeÿÿned template, and these morphed surface models were then used to create a morphed surface average."
In Fig7C ÿÿAverage 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?
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Zhong Jidan