Thanks, I did as you suggested, but got a different error telling me that mris_anatomical_stats cannot be used with fsaverage as it is an average subject.
I am running v 4.2.0. Would I be able to run stats on fsaverage using a new freesurfer version, or is there some other way around this? I am really just trying to compare the surface areas of ROIs contained in different custom annotations. Thanks again for your help, Alex On 05/06/2009 17:15, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > Hi Alex, > > if all you care about is surface area you can probably just copy the > wm.mgz from any subject into the fsaverage/mri dir. Other stats will of > course then be incorrect. You also have to be careful as the fsaverage > surfaces contain less surface area (due to averaging) than individual > subjects. There is a correction factor stored in the fsaverage surface > files you can use if you want, I think mris_info will print it out. > > cheers > Bruce > > > On Fri, 5 Jun 2009, Alex Fornito wrote: > >> Hi, >> I'm playing around with different ways of generating custom annotation files >> using the fsaverage surface, and would like to estimate the surface area of >> each ROI. I tried running mris_anatomical stats, but it seems to required >> wm.mgz, which is not contained in the fsaverage directories (please see >> below). Is there any way around this? I'm really just interested in >> extracting the surface area for each label in my .annot file. >> >> Thanks for your help, >> Alex >> >> mris_anatomical_stats -a lh.test.aparc.annot -f stats_table.txt -log >> logfile.txt fsaverage lh white >> computing statistics for each annotation in lh.test.aparc.annot >> outputting results to logfile.txt... >> reading volume /work/imaging5/af397/twins/fsaverage/mri/wm.mgz... >> ERROR: cannot find /work/imaging5/af397/twins/fsaverage/mri/wm.mgz >> mris_anatomical_stats: could not read input volume >> /work/imaging5/af397/twins/fsaverage/mri/wm.mgz >> No such file or directory >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- Alex Fornito CJ Martin Post-Doctoral Fellow Brain Mapping Unit Department of Psychiatry University of Cambridge Downing Site Downing St, Cambridge UK CB2 3EB Email: af...@cam.ac.uk Phone: +44 (0) 1223 764670 Fax: +44 (0) 1223 336581 Australian Details: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 1 & 2, Alan Gilbert Building 161 Barry St Carlton South 3053 Victoria, Australia Email: forni...@unimelb.edu.au Phone: +61 3 8344 1861 Fax: +61 3 9348 0469 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
