[Freesurfer] mri_segstats: reported volume depends on voxels size
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 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] Bug in mri_segstats.c or MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c
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 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.
Re: [Freesurfer] Bug in mri_segstats.c or MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c
Thanks Doug! New version of mri_segstats is working fine for images with small voxels (<1mm3). --Masaya On 07/16/2012 09:43 AM, Douglas N Greve wrote: > 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 >> >> > ___ 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.
