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
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