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
ry/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
Hi Doug,
Thank you - I have uploaded the files for you.
Eli
From: Eli Johnson
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
case you'd like to modify some of the above information, please use the link
below:
http://gate.nmr.mgh.harvard.edu/filedrop2/?g=ahht5qz16h5
Cheers,
The Martinos Center Web Team
From: Eli Johnson
Sent: Wednesday, 25 January 2017 9:55 AM
To: frees
t;
>
>> 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
>
> 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 D
Ok sure, I will do it tomorrow as I don't have access to the stats file right
now
Many thanks!
From: Eli Johnson
Sent: Thursday, 26 January 2017 6:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
Y
e you sent these files to:
+ gr...@nmr.mgh.harvard.edu
In case you'd like to modify some of the above information, please use the link
below:
http://gate.nmr.mgh.harvard.edu/filedrop2/?g=7z2xk77v3ue
Cheers,
The Martinos Center Web Team
________
From: Eli Johnson
Sent:
sorry for wasting so much
time!). In that case, what does the fourth/highlighted column represent?
Many thanks
Eli
____________
From: Eli Johnson
Sent: Friday, 27 January 2017 10:24 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked regi
Great - that makes sense!
Thanks again for your help in resolving this.
Eli
From: Eli Johnson
Sent: Friday, 27 January 2017 4:59 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
I was reading the fourth
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