Using the fwhm option requires a subject because it needs to take into accnt the surface area. ico7 is not a true subject in the freesurfer sense. However, you should have fsaverage in your distribution, and that is the same as ico7.
The conversion from fwhm to niters is here:
gstd = fwhm/sqrt(log(256.0)); //1.14 is a fudge factor based on empirical fit of nearest neighbor niters = floor(1.14*(4*PI*(gstd*gstd))/(7*avgvtxarea) + 0.5);
The avgvtxarea is the average area for the given subject.
doug
On Thu, 4 Jan 2007, Roberto Toro wrote:
Hi!
I'm trying to smooth thickness data using mri_surf2surf. The thickness vectors are mapped onto ico7, and I would like to smooth the thickness there (ico7). But when I add the --fwhm option to mri_surf2surf (equivalent to --fwhm-trg), mris_surf2surf looks for a real subject called "ico" (ie $SUBJECTS_DIR/ico/surf/lh.white) instead of the oversampled icosahedron...
This is the type of command I'm using (with freesurfer-Darwin-tiger- stable-pub-v3.0.2, mac os 10.4.8):
mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject ico --trgicoorder 7 --fwhm 30 --trgsurfval /Users/roberto/Desktop/bertest-lh.mgh --trg_type mgh
without --fwhm everything goes ok, but including it produces at the end an error like this:
(...) MRISread(/freesurfer/subjects/ico/surf/lh.white): could not open file No such file or directory ERROR: could not read /freesurfer/subjects/ico/surf/lh.white
It looks for a subject ico. I think that I could use --fwhm-src to do the smoothing on bert/lh.white, but then different brain sizes would have different fwhm values after mapped over ico7...
Is there a way of giving an absolute path to the surface used for smoothing? (to /Applications/freesurfer/lib/bem/ic7.tri). Am I doing something wrong?
A last little thing.... how is the number of iterations (à la --nsmooth) computed from the given fwhm?
thanks in advance! (and have a happy new year :)
roberto
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