Re: [Freesurfer] aseg.stats calculations {Disarmed}

2018-11-26 Thread Greve, Douglas N.,Ph.D. 


When total gray is computed, the cerebellum GM volumes are computed by 
simply summing up all the voxels whereas the values that are reported in 
the aseg.stats file include partial volume correction, which is slightly 
different.

On 11/20/2018 02:04 PM, Song, Da-Yea wrote:
>
> External Email - Use Caution
>
> Thank you for pointing that out! I took another look and was able to 
> get the following;
>
> TotalGray (from the aseg.stats) = *751765.612392*
>
> 298534.487540 (lhCortex) + 287682.124852 (rhCortex) +  58860.00 
> (SubCortGray) + 52358.1 (L_cerebellum-cortex) + 52661.8 
> (R_cerebellum-cortex) *= 750096.512392*
>
> There is still a difference of 1669.1. What could account for the 
> difference?
>
> Best,
>
> Da-Yea
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Greve, 
> Douglas N.,Ph.D.
> *Sent:* Tuesday, November 20, 2018 1:50 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] aseg.stats calculations
>
> On 11/20/18 1:37 PM, Song, Da-Yea wrote:
>
> *External Email - Use Caution *
>
> Hello,
>
> I had a question regarding the aseg.stats and was hoping to get
> some help.
>
> 1.How is the TotalGray calculated? On the wiki page it mentioned
> that it is the sum of lhCortex + rhCortex + SubCortGray +
> CerebellumGM. I tried calculating this based on the formula but
> got different results.
>
> a.TotalGray (from the aseg.stats) = *751765.612392*
>
> b.298534.487540 (lhCortex) + 287682.124852 (rhCortex) +
>  58860.00 (SubCortGray) + 49.3682 (L_cerebellum-cortex) +
> 50.1232 (R_cerebellum-cortex) *= 645176.103792*
>
> *Check your value for cerebellum cortex. It should be more like 60,000 
> mm3. You probably are looking at the mean intensity.*
>
> 2.We have subjects that were processed in v4.0.4 and v6.0.0. Since the 
> TotalGray measure did not exist in the v.4.0.4, what could we use to 
> calculate the volume?
>
> How about the above formula?
>
> Thank you so much in advance for your help!
>
> Best,
>
> Da-Yea
>
> 
>
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Re: [Freesurfer] aseg.stats calculations {Disarmed}

2018-11-20 Thread Song, Da-Yea 
External Email - Use Caution

Thank you for pointing that out! I took another look and was able to get the 
following;

TotalGray (from the aseg.stats) = 751765.612392

298534.487540 (lhCortex) + 287682.124852 (rhCortex) +  58860.00 
(SubCortGray) + 52358.1 (L_cerebellum-cortex) + 52661.8 (R_cerebellum-cortex) = 
750096.512392

There is still a difference of 1669.1. What could account for the difference?

Best,
Da-Yea

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas 
N.,Ph.D.
Sent: Tuesday, November 20, 2018 1:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aseg.stats calculations


On 11/20/18 1:37 PM, Song, Da-Yea wrote:

External Email - Use Caution
Hello,

I had a question regarding the aseg.stats and was hoping to get some help.


1.   How is the TotalGray calculated? On the wiki page it mentioned that it 
is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried 
calculating this based on the formula but got different results.

a.   TotalGray (from the aseg.stats) = 751765.612392

b.  298534.487540 (lhCortex) + 287682.124852 (rhCortex) +  58860.00 
(SubCortGray) + 49.3682 (L_cerebellum-cortex) + 50.1232 (R_cerebellum-cortex) = 
645176.103792
Check your value for cerebellum cortex. It should be more like 60,000 mm3. You 
probably are looking at the mean intensity.




2.   We have subjects that were processed in v4.0.4 and v6.0.0. Since the 
TotalGray measure did not exist in the v.4.0.4, what could we use to calculate 
the volume?
How about the above formula?


Thank you so much in advance for your help!

Best,
Da-Yea

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Re: [Freesurfer] aseg.stats calculations

2018-11-20 Thread Greve, Douglas N.,Ph.D. 


On 11/20/18 1:37 PM, Song, Da-Yea wrote:

External Email - Use Caution
Hello,

I had a question regarding the aseg.stats and was hoping to get some help.


1.   How is the TotalGray calculated? On the wiki page it mentioned that it 
is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried 
calculating this based on the formula but got different results.

a.   TotalGray (from the aseg.stats) = 751765.612392

b.  298534.487540 (lhCortex) + 287682.124852 (rhCortex) +  58860.00 
(SubCortGray) + 49.3682 (L_cerebellum-cortex) + 50.1232 (R_cerebellum-cortex) = 
645176.103792

Check your value for cerebellum cortex. It should be more like 60,000 mm3. You 
probably are looking at the mean intensity.



2.   We have subjects that were processed in v4.0.4 and v6.0.0. Since the 
TotalGray measure did not exist in the v.4.0.4, what could we use to calculate 
the volume?

How about the above formula?

Thank you so much in advance for your help!

Best,
Da-Yea

Disclaimer:


The materials in this e-mail are private and may contain Protected Information. 
Please note that e-mail communication is not encrypted by default. You have the 
right to request further emails be encrypted by notifying the sender. Your 
continued use of e-mail constitutes your acknowledgment of these 
confidentiality and security limitations. If you are not the intended 
recipient, be advised that any unauthorized use, disclosure, copying, 
distribution, or the taking of any action in reliance on the contents of this 
information is strictly prohibited. If you have received this e-mail in error, 
please immediately notify the sender via telephone or return e-mail.



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[Freesurfer] aseg.stats calculations

2018-11-20 Thread Song, Da-Yea 
External Email - Use Caution

Hello,

I had a question regarding the aseg.stats and was hoping to get some help.


1.   How is the TotalGray calculated? On the wiki page it mentioned that it 
is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried 
calculating this based on the formula but got different results.

a.   TotalGray (from the aseg.stats) = 751765.612392

b.  298534.487540 (lhCortex) + 287682.124852 (rhCortex) +  58860.00 
(SubCortGray) + 49.3682 (L_cerebellum-cortex) + 50.1232 (R_cerebellum-cortex) = 
645176.103792



2.   We have subjects that were processed in v4.0.4 and v6.0.0. Since the 
TotalGray measure did not exist in the v.4.0.4, what could we use to calculate 
the volume?

Thank you so much in advance for your help!

Best,
Da-Yea

--
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right to request further emails be encrypted by notifying the sender. Your 
continued use of e-mail constitutes your acknowledgment of these 
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recipient, be advised that any unauthorized use, disclosure, copying, 
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