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Hi Alistair The following step is missing in the documentation, sorry: convert_xfm -omat struct2freesurfer.mat -inverse freesurfer2struct.mat Cheers Saad On 16 Aug 2012, at 02:38, Alistair Perry wrote: > Hello, > > I am wishing to perform probx tracking from freesurfer cortical surfaces. Here is the link: > > http://fsl.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html > > Everything is running smoothly, until I want to concentate the freesurfer <> fa, and struct <> freesurfer transformations. > > When I enter this command "convert_xfm -omat fa2freesurfer.mat -concat struct2freesurfer.mat fa2struct.mat " in Linux, it comes up with an error "Could not open matrix file struct2freesurfer.mat". > > I can't find the struct2freesurfer.mat file. It has not been created when performing the transformations. > > Could anyone help? I do have the file freesurfer2struct.mat, perhaps there is an error on the website? > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad