Hi Thomas:
There are no special reasons why i need the surface-based aal template. my
goal is to parcellate surface into thousands of small brain areas, and
construct large-scale cortical network. I have no idea how to segment the
surface directly in FS. But i know the way to segment AAL template to the
specific parcellation level (e.g. AAL-1024 ) i want. that is why i do this.
Best.
zhiliang
At 2013-04-01 12:55:03,"Thomas Yeo" <ytho...@csail.mit.edu> wrote:
>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
><martijnsteenw...@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-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@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" <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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