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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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" 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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

the problem is that the average surface has less surface area than any individual. We keep track of this in the surface file itself (try mris_info on it), then correct for it when we need to.

cheers, Bruce

On Tue, 9 Jun 2009, Alex Fornito wrote:

No, sorry. What is the error?

On 09/06/2009 17:31, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:

...

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" 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >