Hi Nick, The Freesurfer version I use has build stamp freesurfer-Darwin-tiger-i686-stable-pub-v4.0.1
After conversion, read_asc.m doesn't work - seemingly due to a dimension problem. In the code I see that 5 elements are expected for faces and indicies, whereas only 4 elements are provided in the .asc file. I changed lines 45-46 into f = fscanf(fp, '%d', S(3)*4); f = reshape(f, [4 S(3)])'; Using patch in Matlab with v(:,1:3) as vertices and f(:,[1 3 2]) as faces, I get an image of the hippocampus surface. The surface looks good(!) but is a bit rough and 'spiky'. Is this because the segmentation procedure does not employ a smoothness constraint? The aim of all this is to prepare hippocampal volumes for deformation analysis (two groups, two time points). Is the following line of processing appropriate: Topology correction: mri_topologycorrection -label "hippocampus" subject/mri/norm.mgz subject/mri/aseg.mgz aseg_corrected Tesselate surface: mri_tessellate Smooth surface: mris_smooth Convert to ascii for use with Matlab: mris_convert Cheers! Kim. 2007/11/16, Nick Schmansky <[EMAIL PROTECTED]>: > Kim, > > Which version of freesurfer is being used? > > An alternative approach is to convert the surface to ascii: > > mris_convert surface_file surface_file.asc > > where the .asc extension is an output ascii file listing the vertices > and faces. > > Nick > > On Thu, 2007-11-15 at 16:18 +0100, Kim Mouridsen wrote: > > Hi, > > > > We have segmented hippocampus using Freesurfer, and want to generate a > > surface which can be read into matlab. > > > > We use mri_tesselate and mris_smooth. However, the resulting file can > > not be read into matlab using read_surf. The error we get is > > > > ??? Undefined function or variable "vertex_coords". > > > > Error in ==> read_surf at 77 > > vertex_coords = reshape(vertex_coords, 3, vnum)' ; > > > > It seems the 'magic' number is 16777213, whereas only 16777214 and > > 16777215 are supported in read_surf.m > > > > How can we read the result of mris_smooth into matlab? > > > > Thanks! > > > > Kim. > > _______________________________________________ > > 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
