Hi Masaya, you are correct. I've put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux Can you test it out? It also fixes the partial volume computation problem. thanks! doug
On 07/06/2012 02:23 PM, Masaya Misaki wrote: > I've posted a question about a strange behavior of mri_segstats if voxel size > isn't 1 mm3 and --pv > option is used. > > I found a reason of this problem in the source code of mri_segstats.c > (release_5_1_0 branch was checked out from read-only CVS source-code > repository) > > In mri_segstats.c the return value from > MRIvoxelsInLabelWithPartialVolumeEffects is used as the > number of voxels; > > nhits = > MRIvoxelsInLabelWithPartialVolumeEffects > (seg, pvvol, StatSumTable[n].id, NULL, NULL); > vol = nhits*voxelvolume; > > However, MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c returns > volume (e.g. volume += > vox_vol; or volume += vox_vol * pv;), not the number of voxels. > > nhits value is adjusted by voxel volume in mri_segstats.c (vol = > nhits*voxelvolume), so that the > voxelvolume (vox_vol) is multiplied twice. > > The volume reported by mri_segstats, therefore, is too small if the voxel > volume is less than 1 mm^3 > or too large if the voxel volume is larger than 1 mm3. > > Note that this is not a problem when voxel volume is conformed to 1 mm3 > (default option in recon-all). > > I think many of FreeSurfer programs do not support high-resolution (< 1mm3) > image without conforming > to 1 mm3 voxel, but could you fix the problem of mri_segstats? I want to use > mri_segstats with > partial volume correction for high-resolution MRI image. > > Thank you, > > --Masaya > > > On 06/26/2012 08:40 AM, Masaya Misaki wrote: >> Hello all, >> >> I found volume size reported by mri_segstats is changed very much >> depending on voxel size when partial volume correction (--pv option) is >> used. The difference was much larger than that can be explained by the >> difference of image resolution. >> (mri_segstats version is 1.75.22 2011/4/27 in FreeSurfer v5.1.0) >> >> When I performed segmentation for high-resolution image (voxel size = 0.5 >> mm^3), I found all volumes of segmented regions in aseg.stats was too >> small; about 8 times smaller than that was estimated from 1mm^3 conformed >> image. >> >> So I tested the effect of voxel size on mri_segstats. >> At first, recon-all was run with conforming 1mm^3 voxel (default option). >> Then aseg.mgz and norm.mgz were conformed to small voxel size, and >> mri_segstats was applied to the conformed files: >> >> mri_convert aseg.mgz aseg_cs05.mgz -cs 0.5 rt nearest >> mri_convert norm.mgz norm_cs05.mgz -cs 0.5 >> mri_segstats --seg aseg_cs05.mgz --pv norm_cs05.mgz \ >> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ >> --nonempty --excludeid 0 --sum aseg_cs05.stats >> >> (these are just for testing the effect of voxel size, not for actual >> analysis) >> >> All volumes reported in aseg_cs05.stats (for 0.5mm^3 voxel) was about 8 >> times smaller than aseg.stats (for 1mm^3 voxel). So the reported volume >> was scaled with the same ratio as the voxel size. Same effect was observed >> when voxel size was conformed to larger one (e.g. 1.5mm^3); reported >> volumes were about 3 times larger than those for 1mm^3-voxel. The number >> of voxels in the segmented regions (Nvoxels column in aseg.stats) were >> similar across different voxel sizes while voxel sizes are different. >> >> When --pv option was not used, the reported volumes were almost the same >> across different voxel sizes. So the partial volume correction in >> mri_segstats seems to depend on voxel size. >> >> Can I fix this with some missed options or shouldn't I use --pv option >> for the image with voxel size other than 1mm^3? >> >> thanks, >> >> >> -- >> Masaya Misaki Ph.D. >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
