Hi Doug,
Thank you - I have uploaded the files for you. Eli ________________________________ From: Eli Johnson <eli_g_...@hotmail.com> Sent: Friday, 20 January 2017 5:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: Cortical volume from masked region 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 Grevegreve 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
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