Hi Bruce, Thanks, that would be perfect!
I tried increasing the number of smoothing iterations in mris_smooth, and this improves the result, but this is probably not the best way to do it. We would be very happy if you could send us a beta version of your smoothing tools. Cheers, Kim. 2007/11/16, Bruce Fischl <[EMAIL PROTECTED]>: > Hi Kim, > > we do have some tools for smoothing the hippocampal surfaces, but we > haven't distributed them. I could try to get you a beta version if you > like. > > cheers, > Bruce > On Fri, 16 Nov 2007, Kim Mouridsen wrote: > > > 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 > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
