Hi Nick, again thank you your help! That works nicely.
Where to I find the transformation matrix to register my structural volume data to the gii. surface file? I found two matrices in the lh.white.gii (<MatrixData>), but not sure if it fits. I have to use the volume scan and gii suface in matlab for localization and source reconstruction of EEG data (that's why I can't use freeview). Bastian On 2 June 2014 20:50, Nick Schmansky, MGH <ni...@nmr.mgh.harvard.edu> wrote: > Bastian, > > Are you using freeview to display the surface? If so, you will need to > get the newest freeview.bin, which is here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/ > > this has been updated to read the new volume geometry info now included > in the lh.white.gii file, so that it aligns with the volume (via the > c_ras info). > > Nick > > > On Mon, 2014-06-02 at 12:10 +0200, Bastian Cheng wrote: >> Hi, >> >> Ok, thank you! >> >> One additional follow up: >> >> Once I converted the lh.white (freesurfer) to the lh.white.gii >> (gifti), the converted surface (.gii) does not fit on the structural >> scan from freesurfer anymore (neither brain.mgz or orig.mgz or >> nu.omz). >> >> How can I register my freesurfer structural data to the new gifti surface? >> >> I have noticed that a transformation matrix is inserted in the gifti >> file, but have not figured out in which space the image is transformed >> to.. >> >> maybe you could help me clarify that. >> >> Best, >> Bastian. >> >> On 29 May 2014 17:25, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: >> > Hi Bastian >> > >> > do you mean a surface that is only a piece of th original surface? You can >> > use label2patch for that, but I'm not sure if we can convert patches to >> > gifti. You should ask the FSL crew about label2surf though - we can't help >> > with that. >> > >> > cheers >> > Bruce >> > >> > >> > On Thu, >> > 29 May 2014, Bastian Cheng wrote: >> > >> >> Hi Nick, >> >> >> >> That works PERFECTLY! Thank you so much, it has been a big help! >> >> >> >> I hope I may ask you another question: >> >> >> >> I am actually trying to convert each freesurfer-label (from >> >> aparc.annot) into separate surfaces (not gifti-labels) >> >> >> >> So ideally I would convert lh.precentral.label > lh.precentral.gii. >> >> >> >> I have used the command "label2surf", Part of FSL (build 504). (and I >> >> have used the "new" gifti lh.white created with your updated version >> >> as the input surface) >> >> >> >> However, the output gifti does not open in matlab (instead shows the >> >> same error message seen before). >> >> >> >> Now I would guess that whatever changes you made to mris_convert would >> >> have to be applied to "label2surf" as well. I have noticed some >> >> changes in the gifti files with your new mris_convert command. >> >> However, I'm not so familiar with the gifti file structure. >> >> >> >> Maybe I could ask you to have a look into this? >> >> >> >> Also, If there is a easier way to achieve my goal any advise is welcome! >> >> >> >> Again, many thanks for your efforts so far! >> >> Bastian. >> >> >> >> >> >> >> >> >> >> >> >> >> >> On 29 May 2014 02:05, Nick Schmansky, MGH <ni...@nmr.mgh.harvard.edu> >> >> wrote: >> >>> Bastian, >> >>> >> >>> Hi, I've posted a new mris_convert which should solve the problem for >> >>> you. It's built for Centos 6, so if you need it for another platform, >> >>> let me know. It's here: >> >>> >> >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ >> >>> >> >>> Nick >> >>> >> >>> >> >>> >> >>> On Wed, 2014-05-28 at 11:42 +0200, Bastian Cheng wrote: >> >>>> Dear Freesurfer-Experts, >> >>>> >> >>>> I would like to create gifti-surfaces to use in matlab. >> >>>> >> >>>> That's what I am doing so far (latest FS-Version): >> >>>> >> >>>> mris_convert lh.white lh.white.gii >> >>>> >> >>>> I then try to open it using the "gifti" command (g=gifti('file.gii')) >> >>>> (http://www.artefact.tk/software/matlab/gifti/) >> >>>> >> >>>> however, I get an error message from matlab: >> >>>> >> >>>>>>>>>>>>>>> >> >>>> ??? Attempt to reference field of non-structure array. >> >>>> Error in ==> gifti.subsref at 28 >> >>>> varargout{1} = this.data{j}.space.MatrixData; >> >>>> Error in ==> gifti.struct at 17 >> >>>> [values{i,:}] = subsref(this(:), substruct('.',names{i})); >> >>>> Error in ==> gifti.display at 17 >> >>>> eval([display_name ' = struct(this);']); >> >>>>>>>>>>>>>>>>>>> >> >>>> >> >>>> Am I missing something? Is there anything special with the .gii file >> >>>> form FS? >> >>>> >> >>>> here is the surface file I created with mris_convert: >> >>>> http://we.tl/B2n4Ex6ifJ >> >>>> >> >>>> I am able to open the gifti file with freeview. >> >>>> I also updated the gifti-toolbox in matlab to the latest version. >> >>>> >> >>>> >> >>>> Any help is appreciated! >> >>>> _______________________________________________ >> >>>> Freesurfer mailing list >> >>>> Freesurfer@nmr.mgh.harvard.edu >> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>> >> >>>> >> >>> >> >>> >> >>> _______________________________________________ >> >>> 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 >> >> >> >> >> >> >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
