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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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