Rudolph's workaround seems to do the trick. Thanks! On 06/06/2009 18:16, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
> yeah, I guess we disabled it since the surface area isn't representative > of individual subjects. We could either change it to a warning with a > -force flag or something, or you could run mri_annotation2label and run > label_area on the individual labels. > > Do you really want the surface area on the average subject? > > On Sat, 6 Jun 2009, Alex Fornito wrote: > >> 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
