Thanks for the reply. I tried removing the --pv flag as suggested, and the sum of the two split volumes did equal the total un-split volume. However, this value is not equal to value in aseg.stats. I am assuming this is because aseg.stats uses partial volume correction. Is there any way that I can get the sum of the two split values to equal the value in aseg.stats, or is this just something I can't achieve if I want to use the partial volume correction?
Thanks, - Tyler On Jan 5, 2011, at 7:42 PM, Bruce Fischl wrote: > try it without the partial volume correction. It certainly won't be the same > for the split volumes > > On Wed, 5 Jan 2011, Tyler Blazey wrote: > >> Hi, >> >> Is there any way to return the volume for a specific range of slices using >> the tools offered by FreeSurfer? I tried using mri_convert on aseg.mgz to >> select the slices I needed, and then running mri_segstats on the resulting >> volume. >> >> For example: >> >> mri_convert --slice-crop 1 122 aseg.mgz aseg_1_122.mgz >> mri_convert --slice-crop 123 255 aseg.mgz aseg_123_255.mgz >> mri_convert --slice-crop 1 122 norm.mgz norm_1_122.mgz >> mri_convert --slice-crop 123 255 norm.mgz norm_123_255.mgz >> mri_segstats --seg aseg_1_122.mgz --pv norm_1_122.mgz --sum >> ~/Desktop/1_122.txt --ctab $FREESURFER_HOME/ASegStatsLUT.txt --id 17 >> --subject tblaze >> mri_segstats --seg aseg_123_255.mgz --pv norm_123_255.mgz --sum >> ~/Desktop/123_255.txt --ctab $FREESURFER_HOME/ASegStatsLUT.txt --id 17 >> --subject tblaze >> >> When I look at the output, however, the total volume for the the ROI (left >> hippocampus in this case) for the two split volumes (4536 mm3) does not >> equal the value in aseg.stats (4543 mm3). I have tried using different slice >> ranges and different versions of FreeSurfer (4.5, 5.0), and I always have >> the same problem. Is there something that I am doing incorrectly that >> accounts for this discrepancy? Or is there a better way to do all this? >> >> Thanks, as always, for any replies. >> >> - Tyler Blazey >> _______________________________________________ >> 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
