Does this workaround account for the error in the raw area unavoidable
on an average surface? If not, are you aware of it and is it important
for your analysis?
doug
Alex Fornito wrote:
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
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