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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) + 58860.000000 (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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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) + 58860.000000 (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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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) + 58860.000000 (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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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) + 58860.000000 (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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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:
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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) + 58860.000000 (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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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) + 58860.000000 (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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Song, Da-Yea