I believe that someone has created the AAL labels on the Colin 27 brain. These should be able to be transformed to the fsaverage brain.
I've contacted the person who said they had the files and will let you know if I get the files and am able to transform the files. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Mon, Apr 1, 2013 at 6:52 AM, Jürgen Hänggi <j.haen...@psychologie.uzh.ch>wrote: > Hi Zhiliang > > You can use > > mris_make_face_parcellation > > Or > > mris_divide_parcellation > > directly in FreeSurfer to produce your own parcellation scheme > > Cheers > Jürgen > > > On [DATE], "ZhiLiangLong" <[ADDRESS]> wrote: > > 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<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. > >> > >> > >> > >> _______________________________________________ > >> 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. > >> > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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. > >> > > > > ------------------------------ > _______________________________________________ > 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. > > > > > ---------------------------------------------------------------------------- > Jürgen Hänggi, Ph.D. > Division Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > j.haenggi[at]psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > > This e-mail (and any attachment/s) contains confidential and/or privileged > information. If you are not the intended recipient (or have received this > e-mail in error) please notify the sender immediately and destroy this > e-mail. Any unauthorised copying, disclosure or distribution of the > material in this e-mail is strictly forbidden. > > ---------------------------------------------------------------------------- > > > _______________________________________________ > 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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