Hi Doug,
I have re-uploaded the file (see bottom of this email for info):
Along with the default FS output, there are 5 masks, corresponding to frontal, temporal, parietal, occipital and insula regions (e.g. 20001-013-1_std/mri/20001_MNI_lobes_1-in-fs.mgz).
There are 10 surfs corresponding to lh & rh frontal,lh & rh temporal, lh & rh parietal,lh & rh occipital and lh & rh insula (e.g. 20001-013-1_std/surf/20001_MNI_lobes_1-in-fs_surfrh.mgz).
I ran the commands:
mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region1.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region2.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region3.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region4.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region5.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region1.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region2.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region3.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region4.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region5.stats
to extract volumes from the 10 regions. The stats files are located as described in the command.
Also, in the ./20001-013-1_std/stats/ folder are the default FS lobular volumes for comparison.
Thanks again for all of your help, do let me know if I've missed anything again!!
Eli
You recently uploaded the following files to the Martinos Center FileDrop:
+ 20001-013-1_std.tar.gz (252.1 MiB)
Here are the people you sent these files to:
+ greve@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 eli_g_123@hotmail.com Sent: Thursday, 26 January 2017 7:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region
Ok sure, I will do it tomorrow as I don't have access to the stats file right now
Many thanks!
________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Thursday, 26 January 2017 6:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region
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 Phone Number: 617-724-2358 Fax: 617-726-7422
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