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
