Re: [Freesurfer] How to get surface-based AAL template

Hi Zhi Liang,

Out of curiosity, why not just use the FreeSurfer parcellations, so you don't end up with holes in the sulci/gyri?

--Thomas

On Sun, Mar 31, 2013 at 8:28 PM, Martijn Steenwijk martijnsteenwijk@gmail.com wrote:

I faced this problem a while ago. Both MNI to fsaverage, MNI itself and Colin27 didn’t work sufficiently for sampling the labels, all had problems with the registration causing holes in the sulci and gyri ending up in the wrong label. (That might be ‘good’ since AAL is a volumetric atlas; but might also be bad, since you often don’t want to look at an in complete label). I ended up making my own gcs fom a training set with mris_ca_train. Now I can segment surfaces just by calling mris_ca_label which works flawlessly and consistent throughout subjects.

Best,

Martijn

Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens ZhiLiangLong Verzonden: zaterdag 30 maart 2013 16:25 Aan: Garikoitz Lerma-Usabiaga CC: Freesurfer Onderwerp: Re: [Freesurfer] How to get surface-based AAL template

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" garikoitz@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 lagosslong1987@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" garikoitz@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 lagosslong1987@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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