yes, that is a consequence of partial volume correction. If you have a 3 class boundary (two of which are hippocampal subdivisions), we will compute different partial volume fractions than if you have a 2 class boundary. I wouldn't expect it to be a huge effect, but they definitely won't be identical

On Thu, 17 May 2012, Joshua Lee wrote:

We discovered this while subdividing the hippocampus into several subregions using tkmedit to relabel voxels, and finding that these subregions were not adding up to the original volume. I expected some differences, but many deviated more than I had expected. This led me to the test I discussed at the beginning of the thread.

Joshua

On May 16, 2012, at 1:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

hmmm, that is convincing. I don't think there's anything in mri_segstats that knows about the meaning of any of the indices, but maybe Doug can correct me?

On Wed, 16 May 2012, Joshua Lee wrote:

...

Hi Bruce, First, let me add that if I run the mri_segstats without the --pv flag, the two will have identical volumes. This indicates to me that we captured all the voxels into the new label. Joshua

Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Wed, May 16, 2012 at 1:38 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Joshua

 probabilities are computed internally, but not stored nor used
 in volume calcualtions. Are you actually doing a 3D fill? I
 don't think the hippocampus label is guaranteed to be connected.
 Can you try instead replacing every voxel in matlab with the
 hippocampus index to your new one? That I think should give you
 the same results.

 cheers
 Bruce

 On Wed, 16 May 2012, Joshua Lee wrote:

       Suppose I were to open a subject aseg.mgz in
       tkmedit, and use the 3D fill
       tool to relabel the entire left hippocampus
       segmentation to
       'MyNewImaginaryLabel'. If I then re-run the aseg
       stats, should the left
       hippocampus volume from the original aseg.stats be
       identical to the volume
       of MyImaginaryLabel in the newly generated
       aseg.stats?

        Every voxel from the prior label is now assigned to
       the new label; yet, I
       am getting different results (by about 100 voxels in
       the ones I've tried).

       The command Im using to recalculate:
       mri_segstats --seg
       /usr/local/freesurfer/subjects/s02/new_MRI/new/aseg.auto.mgz
       --sum
       /usr/local/freesurfer/subjects/s02/stats/NEWmethod1aseg_Hipp.stats
       --pv
       /usr/local/freesurfer/subjects/s02/mri/norm.mgz
       --excludeid 0
       --brain-vol-from-seg --brainmask
       /usr/local/freesurfer/subjects/s02/mri/brainmask.mgz
       --in
       /usr/local/freesurfer/subjects/s02/mri/norm.mgz
       --in-intensity-name norm
       --in-intensity-units MR --etiv --surf-wm-vol --ctab
       /usr/local/freesurfer/8regions.txt --subject s02;

       Now if I were to relabel 'MyNewImaginaryLabel' to
       'AthirdLabel', and again
       changing every voxel in 'MyNewImaginaryLabel' to the
       new label, the computed
       volumes do not change. This led me to suspect that
       aseg.mgz contains
       probability estimates at each voxel that are then
       subsequently overwritten
       by my tkmedits. However, per a previous conversation
       from a year ago or so
       with Bruce and also the relevant Freesurfer
       documentation this does not seem
       to be the case. Partial volume information is not
       contained within the
       aseg.mgz (right!?), but is computed by mri_segstats
       by comparing border
       voxels with intensities in the norm.mgz. So I am at
       a loss on why these
       should be different.

       This has been replicated in version 4.5 and 5.1
       -
       Joshua Lee
       Graduate Student
       Center for Mind and Brain &
       Department of Psychology
       University of California, Davis
       530.747.3805

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