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 <[email protected]> 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: [email protected] > [mailto:[email protected]] 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" <[email protected]> > 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 <[email protected]> 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" <[email protected]> > 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 <[email protected]> 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 > [email protected] > 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. > > > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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. > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
