Hmm, I did not get an email. Did you put my email address on the upload?
On 1/25/17 4:55 AM, Eli Johnson wrote:
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 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 <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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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.
