Can you upload the subject, the 500_lobes_1-in-fs.mgz file and lh.mask.mgz to
https://gate.nmr.mgh.harvard.edu/filedrop2 and I'll take a look 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 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 you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
