Bastion, Hi, I'm a bit late in this reply. You can use 'mris_info lh.white.gii' to display the matrices in that file. The one labeled 'FS_VOLGEOM_RAS' is the one that will register the surface with the orig.mgz volume file. Note that it will always be three numbers (c_r, c_a, c_s) which just shifts the center of the surface to match the center of the orig volume.
I wouldn't think you would need to use the MNI305 transform, as that's an affine transform to align it in 'talairach' space. N. On Thu, 2014-06-05 at 09:35 +0200, Bastian Cheng wrote: > Problem solved! > > took some effort trying everything out, but finally found a simple > solution by transforming everything into MNI > > Here's how to convert from surface RAS to mni305 > > mni305ras = X*S*inv(K)*ras > X = talairach.xfm > S = scanner vox2ras (mri_info --vox2ras orig.mgz) > K = tkreg vox2ras (mri_info --vox2ras-tkr orig.mgz) > ras = surface ras from gifti file. > > found here: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > > > > > > > On 3 June 2014 09:08, Bastian Cheng <bastianch...@gmail.com> wrote: > > 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
