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
ted
> column represent?
>
>
> Many thanks
>
> Eli
>
> --------
> *From:* Eli Johnson
> *Sent:* Friday, 27 January 2017 10:24 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Cortical
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
ject:* 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
> *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
Sent: Thursday, 26
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
In that case please upload the actual data that is failing.
On 01/26/2017 01:22 PM, Eli Johnson wrote:
> 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 w
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 fr
Sent from my iPhone
> On 26 Jan 2017, at 18:11, Douglas N Greve 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 01/20/2
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 received your data but cannot find either
500_lobes_1-in-fs.mgz or lh.mask.mgz
On 01/25/2017 11:32 AM, Eli Johnson wrote:
>
>
> Yes, I think I got the correct email. Attached is the notification I
> received upon upload.
>
> Thanks
> Eli
>
>
> You recently uploaded the following files to the
Yes, I think I got the correct email. Attached is the notification I received
upon upload.
Thanks
Eli
You recently uploaded the following files to the Martinos Center FileDrop:
+ 20001-013-1_std.zip (251.3 MiB)
Here are the people you sent these files to:
+ gr...@nmr.mgh.harvard.edu
In c
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
*Sent:* Friday, 20 Ja
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
Can you upload the subject, the
500_lobes_1-in-fs.mgz file and lh.mask.mgz to
https://gate.nmr.mgh.harvard.edu/filedrop2
and I'll take a look
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
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
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
On 01/17/2017 11:24 A
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