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.
