Sent from my iPhone
> On 26 Jan 2017, at 18:11, 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
