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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
