When I look in those 5 stats file for rh I see the following values:
89884.3828
34559.8711
51144.5820
53927.2109
6067.4844
These sum up to 2.3558e+05, the value from the aseg.stats file for rh
cort volume is 2.2027e+05, a difference of 7%. What is the problem?
On 01/27/2017 05:24 AM, Eli Johnson wrote:
>
> 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:
>
> + gr...@nmr.mgh.harvard.edu
>
> 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 <eli_g_...@hotmail.com>
> *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 <eli_g_...@hotmail.com>
> *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
> <gr...@nmr.mgh.harvard.edu> 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 <eli_g_...@hotmail.com>
> >> *Sent:* Tuesday, 17 January 2017 4:24 PM
> >> *To:* freesurfer@nmr.mgh.harvard.edu
> >> *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
> >> 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: 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
> > 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
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> > but does not contain patient information, please contact the sender
> and properly
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> >
>
>
> _______________________________________________
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--
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: 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/
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