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
This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.