Doug - thanks that sounds well worth trying. the labels we have have arbitrary spatial resolution in the saggital plane, and 1mm gaps between saggital slices.
In general in this project we are using an isotropic resolution of 0.25mm. To generate surfaces in freesurfer I have to downsample to 0.35mm (to fit into 256) in applying the procedure you suggest a) is it possible to use a volume with a dimension > 256? b) is it possible to use a non-isotropic resolution? playing around with non-isotropic resolutions, projection fractions and vote would yield different results. c) can mri_aparc2aseg output a volume > 256? 0.35 isotropic will be ok. we'd prefer 0.25 if we can. best Colin > ---------- Forwarded message ---------- > From: Douglas Greve <[email protected]> > To: <[email protected]> > Cc: > Date: Sun, 23 Jun 2013 20:03:09 -0700 > Subject: Re: [Freesurfer] ribbon label volume mapping > > You could run mri_vol2surf at different projection fractions (and using > nearest neighbor interp). This will create a set of files, one for each > projection fraction. You can then run mri_concat with the --vote option to > get you the most frequently occurring label. You could then use > mris_seg2annot to create an annotation. > > If you want to go the other way, you will need to combine your labels into > an annotation (mris_label2annot), then convert that into a volume with > mri_aparc2aseg. > > doug > > > On 6/22/13 10:08 AM, Colin Reveley wrote: > > If one has a volume of integers, each representing a cortical area, > can one map that to the surface as a set of labels, in a smart way that > e.g. takes the mode of the voxels that lie on the vector between equivalent > white and pial nodes (ie uses curvature and thickness information, tacitly > or explicitly)? > > the labels are not exactly on the ribbon. There are many voxels outside > the ribbon that are non zero. Like caudate etc. > > and some voxels that are within the ribbon but are zero because the > label data is was/is non-isotropic originally (which is the problem we want > to solve in fact). > > that would be great. > > Now let's say you already have labels on a mesh. > > can you generate a ribbon volume of labels, i.e. the opposite operation > to what I enquire about above (opposite but not inverse operation)? > > This is work in rhesus. So my pipeline is very barebones indeed, really > just > > mri_normalize > ... > mri_tesselate > mri_inflate/smooth/sphere > mris_fix_topology <-noaseg -noaprc> > mris_make_surfaces <-naseg -noaparc> > > I only have access to what is generated by that sequence or what I can > subsequently generate. > I can generate a freesurfer like ribbon with mris_fill. > > My understanding of labels and data mapping in general in freesurfer is > very poor. > > Maybe adapting one of your matlab scripts might be an idea, if there is > not another way? > > many thanks, > > Colin, > Sussex > > > _______________________________________________ > Freesurfer mailing > [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >
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