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Hello freesurfer experts,
I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other.
If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly.
Thank you in advance for your time,
Tara Palin
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I'm not sure what your question is. You can't just average the ROI values to get the global value unless you weight by the ROI size.
On 8/21/2020 2:55 PM, Palin, Tara wrote:
External Email - Use Caution
Hello freesurfer experts,
I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other.
If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly.
Thank you in advance for your time,
Tara Palin
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I was asking if the Mean Thickness value and the Pial Surface Area values at the top of the aparc.stats file that is generated when running freesurfer are the global measures. And if they are, I got very close values on multiple different apar.stats files by using the Surface Area and AvgThick ROI values printed at the bottom of the file. Basically, how are those values stated in the first sentence being calculated.
Thank you.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, August 21, 2020 6:42:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Global surface area and global thickness values
KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe. ________________________________ I'm not sure what your question is. You can't just average the ROI values to get the global value unless you weight by the ROI size.
On 8/21/2020 2:55 PM, Palin, Tara wrote:
External Email - Use Caution
Hello freesurfer experts,
I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other.
If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly.
Thank you in advance for your time,
Tara Palin
________________________________ 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!CR-rLYS5ufxg2No!L_0CP6RZisrsXKiNCmlZCJXODPe_i2d0VgZM-RdqRvzxAuleEZq8DdYzr3kULOTgv4o$
The average thickness is the average over all the vertices in the cortex.label The total surface area is the sum of all the triangles that have all three corners in the cortex.label
On 8/24/2020 9:35 AM, Palin, Tara wrote:
External Email - Use Caution
I was asking if the Mean Thickness value and the Pial Surface Area values at the top of the aparc.stats file that is generated when running freesurfer are the global measures. And if they are, I got very close values on multiple different apar.stats files by using the Surface Area and AvgThick ROI values printed at the bottom of the file. Basically, how are those values stated in the first sentence being calculated.
Thank you.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Friday, August 21, 2020 6:42:38 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Global surface area and global thickness values KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe.
I'm not sure what your question is. You can't just average the ROI values to get the global value unless you weight by the ROI size.
On 8/21/2020 2:55 PM, Palin, Tara wrote:
External Email - Use Caution
Hello freesurfer experts,
I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other.
If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly.
Thank you in advance for your time,
Tara Palin
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "urldefense.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you very much for your help.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, August 24, 2020 10:15:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Global surface area and global thickness values {Disarmed}
KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe. ________________________________ The average thickness is the average over all the vertices in the cortex.label The total surface area is the sum of all the triangles that have all three corners in the cortex.label
On 8/24/2020 9:35 AM, Palin, Tara wrote:
External Email - Use Caution
I was asking if the Mean Thickness value and the Pial Surface Area values at the top of the aparc.stats file that is generated when running freesurfer are the global measures. And if they are, I got very close values on multiple different apar.stats files by using the Surface Area and AvgThick ROI values printed at the bottom of the file. Basically, how are those values stated in the first sentence being calculated.
Thank you.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Friday, August 21, 2020 6:42:38 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Global surface area and global thickness values
KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe. ________________________________ I'm not sure what your question is. You can't just average the ROI values to get the global value unless you weight by the ROI size.
On 8/21/2020 2:55 PM, Palin, Tara wrote:
External Email - Use Caution
Hello freesurfer experts,
I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other.
If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly.
Thank you in advance for your time,
Tara Palin
________________________________ 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "urldefense.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!CR-rLYS5ufxg2No!L_0CP6RZisrsXKiNCmlZCJXODPe_i2d0VgZM-RdqRvzxAuleEZq8DdYzr3kULOTgv4o$
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!CR-rLYS5ufxg2No!Lwx5VTWmvvdHtI228UfYzAW24rMPrh7aqzZNP7Zbkjsh0LdEBxDhqDinCTrf4ZVcthc$
External Email - Use Caution
Again, thank you for your explanation of how these variables are calculated. However, the the main question still left is, are these values the most representative of the whole cerebral surface area and the whole cerebral thickness for both the left and right hemispheres?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, August 24, 2020 10:15:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Global surface area and global thickness values {Disarmed}
KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe. ________________________________ The average thickness is the average over all the vertices in the cortex.label The total surface area is the sum of all the triangles that have all three corners in the cortex.label
On 8/24/2020 9:35 AM, Palin, Tara wrote:
External Email - Use Caution
I was asking if the Mean Thickness value and the Pial Surface Area values at the top of the aparc.stats file that is generated when running freesurfer are the global measures. And if they are, I got very close values on multiple different apar.stats files by using the Surface Area and AvgThick ROI values printed at the bottom of the file. Basically, how are those values stated in the first sentence being calculated.
Thank you.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Friday, August 21, 2020 6:42:38 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Global surface area and global thickness values
KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe. ________________________________ I'm not sure what your question is. You can't just average the ROI values to get the global value unless you weight by the ROI size.
On 8/21/2020 2:55 PM, Palin, Tara wrote:
External Email - Use Caution
Hello freesurfer experts,
I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other.
If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly.
Thank you in advance for your time,
Tara Palin
________________________________ 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "urldefense.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!CR-rLYS5ufxg2No!L_0CP6RZisrsXKiNCmlZCJXODPe_i2d0VgZM-RdqRvzxAuleEZq8DdYzr3kULOTgv4o$
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!CR-rLYS5ufxg2No!Lwx5VTWmvvdHtI228UfYzAW24rMPrh7aqzZNP7Zbkjsh0LdEBxDhqDinCTrf4ZVcthc$
Yes!
On 8/26/20 9:30 AM, Palin, Tara wrote:
External Email - Use Caution
Again, thank you for your explanation of how these variables are calculated. However, the the main question still left is, are these values the most representative of the whole cerebral surface area and the whole cerebral thickness for both the left and right hemispheres?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, August 24, 2020 10:15:10 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Global surface area and global thickness values {Disarmed} KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe.
The average thickness is the average over all the vertices in the cortex.label The total surface area is the sum of all the triangles that have all three corners in the cortex.label
On 8/24/2020 9:35 AM, Palin, Tara wrote:
External Email - Use Caution
I was asking if the Mean Thickness value and the Pial Surface Area values at the top of the aparc.stats file that is generated when running freesurfer are the global measures. And if they are, I got very close values on multiple different apar.stats files by using the Surface Area and AvgThick ROI values printed at the bottom of the file. Basically, how are those values stated in the first sentence being calculated.
Thank you.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Friday, August 21, 2020 6:42:38 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Global surface area and global thickness values KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe.
I'm not sure what your question is. You can't just average the ROI values to get the global value unless you weight by the ROI size.
On 8/21/2020 2:55 PM, Palin, Tara wrote:
External Email - Use Caution
Hello freesurfer experts,
I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other.
If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly.
Thank you in advance for your time,
Tara Palin
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "urldefense.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "urldefense.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N. Greve
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Palin, Tara