In that case please upload the actual data that is failing.
On 01/26/2017 01:22 PM, Eli Johnson wrote: > 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 >> 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
