Oh, sorry, I see the confusion. Those values are bogus when a surface is used as the input. I originally wrote segstats to handle volumetric data. It works with surface data, but it creates this confusion. In this case, it is the 6th column you want.
On 01/27/2017 11:59 AM, Eli Johnson wrote: > > Hi Doug, > > > I was reading the fourth column in the stats files as the volumes > (highlighted in yellow), as that seems to correspond to the volume_mm3 > label when the columns are lined up. Also, when I run asegstats2file > with the 'rh.vol_region1.stats' file specified alongside 'volume' as > the measure, the output is the fourth(highlighted) number in the stats > files. > > > region 1 rh: > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev > Min Max Range > > 1 1 49885 49885.0 Seg0001 88695.1094 1.1755 0.0000 > 19.4994 19.4994 > > region 2 rh: > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev > Min Max Range > > 1 1 20761 20761.0 Seg0001 29523.0742 0.9522 0.0000 > 11.5547 11.5547 > > region 3 rh: > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev > Min Max Range > > 1 1 35995 35995.0 Seg0001 57553.2656 1.0586 0.0000 > 10.9540 10.9540 > > region 4 rh: > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev > Min Max Range > > 1 1 27060 27060.0 Seg0001 56422.7969 1.5332 0.0000 > 22.9446 22.9446 > > region 5 rh: > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev > Min Max Range > > 1 1 2873 2873.0 Seg0001 5976.5181 1.4734 0.0424 > 11.5412 11.4987 > > > If it's simply a case of me misinterpreting the stats file, and column > 6 being the volume then I agree - there is no problem (and sorry for > wasting so much time!). In that case, what does the fourth/highlighted > column represent? > > > Many thanks > > Eli > > ------------------------------------------------------------------------ > *From:* Eli Johnson <[email protected]> > *Sent:* Friday, 27 January 2017 10:24 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Cortical volume from masked region > > Hi Doug, > > > I have re-uploaded the file (see bottom of this email for info): > > Along with the default FS output, there are 5 masks, corresponding to > frontal, temporal, parietal, occipital and insula regions (e.g. > 20001-013-1_std/mri/20001_MNI_lobes_1-in-fs.mgz). > > There are 10 surfs corresponding to lh & rh frontal,lh & rh temporal, > lh & rh parietal,lh & rh occipital and lh & rh insula (e.g. > 20001-013-1_std/surf/20001_MNI_lobes_1-in-fs_surfrh.mgz). > > > I ran the commands: > > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surfrh.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum > ./${i}-013-1_std/rh.vol_region1.stats > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surfrh.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum > ./${i}-013-1_std/rh.vol_region2.stats > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surfrh.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum > ./${i}-013-1_std/rh.vol_region3.stats > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surfrh.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum > ./${i}-013-1_std/rh.vol_region4.stats > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surfrh.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum > ./${i}-013-1_std/rh.vol_region5.stats > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surf.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum > ./${i}-013-1_std/lh.vol_region1.stats > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surf.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum > ./${i}-013-1_std/lh.vol_region2.stats > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surf.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum > ./${i}-013-1_std/lh.vol_region3.stats > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surf.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum > ./${i}-013-1_std/lh.vol_region4.stats > mri_segstats --seg > ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surf.mgz --id 1 > --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum > ./${i}-013-1_std/lh.vol_region5.stats > > > > to extract volumes from the 10 regions. The stats files are located as > described in the command. > > > Also, in the ./20001-013-1_std/stats/ folder are the default FS > lobular volumes for comparison. > > > Thanks again for all of your help, do let me know if I've missed > anything again!! > > > Eli > > > > > > > You recently uploaded the following files to the Martinos Center FileDrop: > > + 20001-013-1_std.tar.gz (252.1 MiB) > > Here are the people you sent these files to: > > + [email protected] > > In case you'd like to modify some of the above information, please use > the link below: > > http://gate.nmr.mgh.harvard.edu/filedrop2/?g=7z2xk77v3ue > > Cheers, > The Martinos Center Web Team > ------------------------------------------------------------------------ > *From:* Eli Johnson <[email protected]> > *Sent:* Thursday, 26 January 2017 7:13 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Cortical volume from masked region > > Ok sure, I will do it tomorrow as I don't have access to the stats > file right now > > Many thanks! > > ------------------------------------------------------------------------ > *From:* Eli Johnson <[email protected]> > *Sent:* Thursday, 26 January 2017 6:22 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Cortical volume from masked region > > Hi Doug, > > Yes, I have a series of masks that I have created to cover the whole > cortex, but I want to examine the regions separately. Each region > outputs a volume much smaller than I would expect given the volumes > from aseg stats for the whole cortex. That is to say, when I combine > the volume from each region although I would expect it to be different > to the volume from aseg stats (aseg stats is of course highly > optimized), it's a lot smaller than expected - around half the size. > > Sorry for not being more clear! > Thanks > > > On 26 Jan 2017, at 18:11,y Douglas N Greve > <[email protected]> wrote: > > > > In looking at your mask, it covers only half (or less) of the brain. > > This would explain why the total volume you get from the mask is much > > lesss than the total gm volume reported in aseg.stats. > > > > > >> On 01/20/2017 12:08 PM, Eli Johnson wrote: > >> > >> *Hi Doug,* > >> > >> * > >> * > >> > >> *Thanks a lot for your help!* > >> > >> * > >> * > >> > >> *I have run these commands and they complete with no problems. I can > >> also view the region overlaid on a surface and this looks ok, however > >> the volumes that are extracted from mri_segstats are much lower than > >> expected - around half the volume expected, and they don't seem in > >> line with the volumes automatically extracted (i.e. total cortical gm > >> volume from the aseg.stats file). Any thoughts on why this might be?* > >> > >> * > >> * > >> > >> *Many thanks!* > >> > >> *Eli > >> * > >> > >> * > >> * > >> > >> * > >> * > >> > >> * > >> * > >> > >> *Douglas N Greve*greve at nmr.mgh.harvard.edu > >> > <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E> > >> /Wed Jan 18 15:30:45 EST 2017/ > >> > >> * Previous message: [Freesurfer] Cortical volume from masked region > >> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html> > >> * Next message: [Freesurfer] installation fail :( > >> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html> > >> * *Messages sorted by:* [ date ] > >> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559> > >> [ thread ] > >> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559> > >> [ subject ] > >> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559> > >> [ author ] > >> > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559> > >> > >> > >> > >> I would probably map the mask to the surface,eg, > >> > >> mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i > >> scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz > >> > >> The run > >> > >> mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o > >> lh.vol.stats > >> > >> > >> > ------------------------------------------------------------------------ > >> *From:* Eli Johnson <[email protected]> > >> *Sent:* Tuesday, 17 January 2017 4:24 PM > >> *To:* [email protected] > >> *Subject:* Cortical volume from masked region > >> > >> Hi all, > >> > >> > >> I am trying to extract the volume from a FreeSurfer segmented scan > >> within a pre-registered mask region, but only within the cortex, and > >> wanted to check my command. > >> > >> > >> The mask is a binary mask (value of 1 across the mask) and is in the > >> same space as the orig.mgz file. It covers part of the frontal lobe. > >> > >> > >> I have run: > >> > >> mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i > >> ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum > >> > >> > >> This has output a text file with a value of 495563 mm3 in the last row. > >> > >> > >> I wanted to check whether this is the correct command to extract only > >> cortical GM within this mask. If this is correct, should be adding > >> other flags (e.g. -pv). I have searched the mailing list and the > >> options for mri_segstats, but I'm not 100% confident in what I've done > >> - so any tips would be greatly appreciated. > >> > >> > >> Many thanks > >> Eli > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> [email protected] > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > [email protected] > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
