Rudolph's workaround seems to do the trick. Thanks!
On 06/06/2009 18:16, "Bruce Fischl" fischl@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" fischl@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
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