The partial volume correction is done based on the intensity and label of the surrounding voxels. By using aparc+aseg you change the label of the surrounding structures and it changes the PV correction. Use aseg.mgz and not aparc+aseg doug

On 05/09/2014 05:27 AM, Schreiber, Stefanie wrote:

Dear all,

For the evaluation of the subcortical volumes we executed ‘mri_segstats’ on ‘aseg.mgz’ and for comparison on ‘aparc+aseg.mgz’ in a number of individuals. Apparently the volume of subcortical structures, like the hippocampus, is calculated as the same values if calculated (without partial volume correction) from ‘aseg.mgz’ and ‘aparc+aseg.mgz’. However, when partial volume correction is applied, the resulting values for e.g. hippocampal volumes differ between the ‘mri_segstats’ calculation for ‘aseg.mgz’ and ‘aparc+aseg.mgz’. How could those differences resulting from the partial volume correction in these cases be explained?

The command used to calculate the subcortical volumes with partial volume correction was: mri_segstats --seg ./mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --excludeid 0 --sum ./stats/my.test.stats --pv ./mri/norm.mgz

Previously we have been using the subcortical volumes from ‘aseg.stats’, which, as I understand it, is generated by recon-all from ‘aseg.mgz’ via ‘mri_segstats’ (with partial volume correction). From your experience, would it be also valid to use subcortical volumes generated by applying ‘mri_segstats’ (with partial volume correction) on ‘aparc+aseg.mgz’, even though the resulting values might differ from the values in aseg.stats?

Thank you very much in advance,

Steffi Schreiber

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