The volumes in aseg.stats are in native space.

doug

On 12/04/2013 11:21 AM, Jonathan Harlap wrote:

I hope this question doesn't seem too dim, but hopefully someone can
give me a simple answer…

I'm currently interested in subcortical structure volumes,
particularly hippocampus, so I'm looking in my subjects dirs at
stats/aseg.stats to get those values. It's not clear to me if those
measurements are in native or FS space and when I skim over the code
for mri_segstats I don't see anything in there that applies a scaling
factor to take into account the scale parameter of the native space to
FS space transform, so I've been assuming that the volumes reported in
aseg.stats are actually in FS space although that seems odd to me. So
first off, are aseg.stats measurements in native or FS space?

As a naive first attempt to calculate the scale factor myself I simply
ran xfm2param on mri/transforms/talairach.xfm and then multiplied
together all three scale factors to end up with something I could
multiply the aseg.stats results by to get back to native space
measurements. In one particular case I got a result of about 1.26.
However, when I follow the directions at
http://freesurfer.net/fswiki/FsAnat-to-NativeAnat to move the aseg.mgz
into native space and then use mincstats to generate a histogram of
the label values in the segmentation and compare that histogram to the
same histogram generated from the FS space aseg.mgz, I find the values
I get back from both files (a) don't match aseg.stats measurements and
(b) are not scaled by anywhere close to 126% relative to each other.
The former is undoubtedly a result of mri_segstats taking partial
volume effects into account when calculating measurements, which is
great, but the latter is genuinely surprising and makes me wonder if
I'm making a bad assumption about what talairach.xfm is really
supposed to represent.

So - the real question of the day, how do I reliably get these
subcortical volume measurements in native space using FreeSurfer?

Cheers,
Jonathan

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Douglas N. Greve, Ph.D.

MGH-NMR Center

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