Sorry to bug again with this issue when converting the freesurfer surface to GIFTI using mris_convert the surface is shifted in space. Does anyone know how to transform it to freesurfer space?
Thanks! Shani On Tue, Sep 3, 2013 at 12:34 PM, Saad Jbabdi <s...@fmrib.ox.ac.uk> wrote: > You need to convert your surface file into a format that workbench > understand (GIFTI): > > mris_convert lh.whiteinraw lh.whiteinraw.surf.gii > > Cheers > Saad > > > On 3 Sep 2013, at 10:57, Shani Ben Amitay <shani.hol...@gmail.com> wrote: > > Thank you! > Still somehow I haven't manage to make it work when I ran the suggested > command I get an error saying : > ERROR, Command Failed: Parse Error while reading lh.whiteinraw: error > occurred while parsing element line number: 1 column number: 1. > Any advise? > > Thanks again > > Shani > > > > On Mon, Sep 2, 2013 at 10:18 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu>wrote: > >> thanks Matt >> Bruce >> On Mon, 2 Sep 2013, Glasser, Matthew wrote: >> >> > Hi Bruce, >> > >> > Connectome Workbench commandline utilities can do this with FSL warp >> > fields: >> > >> > wb_command -surface-apply-warpfield >> > >> > One needs to use the inverse warp as the <warpfield> argument and the >> > forward warp as the -fnirt <forward-warp>. >> > >> > Peace, >> > >> > Matt. >> > >> > On 9/2/13 11:19 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> > >> >> A veritable game of telephone! Thanks Jesper. Matt? >> >> >> >> On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >> >> >>> Hi guys, >> >>> I didn't think we had any tools for doing that, and said so much on >> the >> >>> FSL >> >>> mailbase. But apparently the WashU people has something that does just >> >>> that >> >>> for you. I think the best person to contact about the details is Matt >> >>> Glasser. >> >>> >> >>> J >> >>> >> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <s...@fmrib.ox.ac.uk> >> >>> wrote: >> >>> >> >>> Hi In Probtrackx, this is done internally. >> >>> If you just want to transform the vertex coordinates, then I think >> >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >> >>> knows better. >> >>> >> >>> Cheers, >> >>> Saad >> >>> >> >>> >> >>> >> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> >>> wrote: >> >>> >> >>> you might check on the FSL list. I think I've seen some >> >>> traffic indicating that there are some tools for doing >> >>> this. I'l cc Saad as he might know >> >>> >> >>> cheers >> >>> Bruce >> >>> >> >>> >> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >> >>> >> >>> Hi Shani, I don't think you can apply a FNIRT >> >>> transform to a surface. >> >>> doug >> >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >> >>> Dear freesurfer people, >> >>> Any idea whether I can apply transformation >> >>> that was calculated by fsl >> >>> fnirt on the white/pial surfaces calculated >> >>> using the freesurfer >> >>> stream? >> >>> Thanks! >> >>> Shani >> >>> _______________________________________________ >> >>> 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. >> >>> >> >>> >> >>> >> >>> -- >> >>> Saad Jbabdi >> >>> University of Oxford, FMRIB Centre >> >>> >> >>> JR Hospital, Headington, OX3 9DU, UK >> >>> (+44)1865-222466 (fax 717) >> >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >> >>> >> >>> >> >>> >> > >> > >> > ________________________________ >> > The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> > >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > >
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