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 <fis...@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 >> >> >> > > 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<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. >
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