Hi Doug This is my command line:
mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh In the past, you recommended smoothing the data with mri_surf2surf instead of with mris_anatomical_stats. For that purpose, I run the following command: mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex But the following error occurred: [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% foreach s ( MOREA_* ) foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval lh.area.15.mgh --cortex foreach? end srcsubject = MOREA_KG002 srcval = (null) srctype = trgsubject = MOREA_KG002 trgval = lh.area.15.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg Loading source data Reading surface file /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area nquads=9895939, nvertices=399 ERROR: MRISread: file '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more faces than vertices! Probably trying to use a scalar data file as a surface! Thanks for help in advance Cheers Jürgen On [DATE], "Douglas Greve" <[ADDRESS]> wrote: > what is your command line? > doug > > On 6/6/12 5:25 AM, Jürgen Hänggi wrote: >> Dear FS experts >> >> I have done group comparisons wrt thickness and surface area. The >> found clusters were written out as annotations, transformed into each >> individual space, and then the corresponding values were extracted. >> >> When using mris_anatomical_stats, values are different for thickness maps >> depending whether I used the --nsmooth 15 option or not. So good >> so far. >> >> However, when using the same command (see below) for ?h.area files, >> extracted values are the same whether or not I used the --nsmooth option. >> >> It seems that the --nsmooth option in mris_anatomical_stats does not >> affect (smooth) the surface area maps. >> >> Is there any solution to also smooth surface area maps with >> mris_anatomical_stats? >> >> I use the Mac FS 5.1.0 version >> >> Thanks in advance >> Best regards >> Jürgen Hänggi >> >> >> ---------------------------------------------------------------------------- >> Jürgen Hänggi, Ph.D. >> Division Neuropsychology >> Institute of Psychology >> University of Zurich >> Binzmuehlestrasse 14, PO Box 25 >> 8050 Zurich, Switzerland >> 0041 44 635 73 97 (phone office) >> 0041 76 445 86 84 (phone mobile) >> 0041 44 635 74 09 (fax office) >> BIN 4.D.04 (office room number) >> j.haenggi[at]psychologie.uzh.ch (email) >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> http://www.juergenhaenggi.ch (private website) >> >> This e-mail (and any attachment/s) contains confidential and/or privileged >> information. If you are not the intended recipient (or have received this >> e-mail in error) please notify the sender immediately and destroy this >> e-mail. Any unauthorised copying, disclosure or distribution of the >> material in this e-mail is strictly forbidden. >> ---------------------------------------------------------------------------- >> >> >> >> >> _______________________________________________ >> 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 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ---------------------------------------------------------------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
