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 530.747.3805The 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.