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 >
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