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 <greve@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/
>>
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>>
>>
>> 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_123@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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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
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>
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