Dear Gari:
    Thank you for give me suggestions patiently. i figured it out as you 
suggested. it works well. I have one more question: Do you know there are 
published papers which use the surface-based aal template (or something like 
this) to do research (e.g. cortical network analysis based on this template)?
 
Best wishes.
zhiliang



At 2013-03-29 15:34:02,"Garikoitz Lerma-Usabiaga" <gariko...@gmail.com> wrote:

Hi Zhiliang,
1- well, I just recon-all-ed their subject again with the newest version. 
Recon-all -s Colin -all
2- maybe Doug or some other will answer this question better. I don't know the 
exact differences between fs mni305 and fs mnicolin27. What I know is that 
going the fsaverage path I couldn't obtain reliable transformations of the AAL 
labels. I think this was because fsaverage is very smoothed. Spm_register and 
vol2surf weren't working well. 


The thing is, for group analysis, you can use Colin (or any other), as I 
understood it. When you use -qcache your data goes to fsaverage, but you can do 
it manually and specify that you want Colin instead (maybe someone can confirm 
it). If you are going to use just the AAL average CTs, then you just need to 
use surf2surf or label2label and you won't need fsaverage at all.


3- well, the spm single subject and Colin from Surfrend are the same subject 
but not exactly the same image. You do bbregister to them and obtain your 
register.dat matrix (you name it), and it goes from 2mm to 1mm and has some 
minimal translation. If you see both T1-s with tkregister you will see that 
they are almost the same (the spm version a little bit blurred, because of the 
resolution). You use this register.dat when doing vol2surf of the AAL.nii to 
your AAL.mgh surface ROI.


Hope this helps!
Gari

On 27/03/2013, at 14:06, ZhiLiangLong <lagosslong1...@163.com> wrote:


Dear Br:
   Thanks for your help. I have downloaded Colin 27 subject, and the Surfrend 
toolbox. But I still have some questions about the process.
   1. You said I need transform the Colin 27 to the latest FS version (v.5.2). 
But i don't know how to do this. It is helpful if you can provide some 
information.
  2. How does the Colin 27 space differs from fsaverage MNI305 space? The group 
analysis of cortical thickness is conducted in fsaverage space, after importing 
AAL ROI into Colin 27 space, should i  transform the obtained ROI into 
fsaverage space?
 3. i don't understand what is the register.dat between COlin 27 and SPM-s 
single subject t1.nii used for? I have tried the Surfrend, and found there was 
no entry for input of register file during the processing.

Looking forward to your reply.
Best wishes.

zhiliang




At 2013-03-27 13:29:01,"Garikoitz Lerma-Usabiaga" <gariko...@gmail.com> wrote:

Hi, 
In my case transformation to fsaverage did not work very well. What I did was:
-  from Surfrend page download Colin 27 subject and transform it to the latest 
version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and SPM-s 
single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined 
in Colin 27. As they are the same subject, the registering is very good.
- now you can import every AAL ROI (in .nii form) to an annotation or in the 
form of individual labels to your FS Colin 27, using the newly created 
registering file.
- now you can use surf2surf or label2label to go to your subjects and obtain 
stats.


Br!

On 27/03/2013, at 05:35, ZhiLiangLong <lagosslong1...@163.com> wrote:


Hi all;
      I need a suface-based aal template which is compatible with FS surface 
file. Is there a way i can get the surface-based aal template? I have an idea, 
that is to just transform the AAL template (.nii file) in MNI space onto the 
surface template (e.g. fsaverage template) in FS. Is it correct? if in this 
case, how can i do the transformation?
 
Any suggestions appreciated.
Besh wishes.



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