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:
+ [email protected]
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 <[email protected]>
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 <[email protected]>
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 <[email protected]> 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/
>>
>> * 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 <[email protected]>
>> *Sent:* Tuesday, 17 January 2017 4:24 PM
>> *To:* [email protected]
>> *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
>> [email protected]
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [email protected]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> [email protected]
> 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.
>
_______________________________________________
Freesurfer mailing list
[email protected]
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.
