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Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Yes the pial surface changed and the white did not. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDU Enviado: martes, 9 de noviembre de 2021 14:49 Para: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
⚠ Caution: External sender
The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1M5P_hTLmY0o3y0f3WBejaH2eWBLycCxB5JOeXiur6T_fRT...https://secure-web.cisco.com/18jwzbq6koFUTgWZ3UTwDDmlFp3S7nENHKQKswzAWRKaGqzqQN1trIM1DDK8KzIrBAkv8mTtDRKWsd80P2yCOv-Np-OmYSj3xiGHzQG2mabATiVM1uPc6PjwXCJ0X-tBXdzlOX7SgZyYYHU6N93WTwOEBar4IZVFPvc01svJzhki4aI1mQ7MrWPozbUlm43LGrEqEaSFLxK35Nk6mMcC0hjQOC11riEW0QECyGC8BHuU4Tkcb-837ldeX4SBiIoCjX_tzoRGCPl3sTxmWx-RE9N1sZsVp4TZWWAohf89L7gtAshZIp54PbgmU8-bwevZV/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cg.leal%2540ucl.ac.uk%257Cb69c988d010e48c55add08d9a3902b09%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637720661863289918%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D2652Ptojb17Rbe%252FgPVm4G1%252FaUVjsEOkmPS3GaiWfsik%253D%26reserved%3D0
Were the stats files regenerated? Check the modification date
On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Yes the pial surface changed and the white did not.
*De:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDU *Enviado:* martes, 9 de noviembre de 2021 14:49 *Para:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
⚠ Caution: External sender
The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/18jwzbq6koFUTgWZ3UTwDDmlFp3S7nENHKQKswzAWRKaGqzqQN1trIM1DDK8KzIrBAkv8mTtDRKWsd80P2yCOv-Np-OmYSj3xiGHzQG2mabATiVM1uPc6PjwXCJ0X-tBXdzlOX7SgZyYYHU6N93WTwOEBar4IZVFPvc01svJzhki4aI1mQ7MrWPozbUlm43LGrEqEaSFLxK35Nk6mMcC0hjQOC11riEW0QECyGC8BHuU4Tkcb-837ldeX4SBiIoCjX_tzoRGCPl3sTxmWx-RE9N1sZsVp4TZWWAohf89L7gtAshZIp54PbgmU8-bwevZV/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cg.leal%2540ucl.ac.uk%257Cb69c988d010e48c55add08d9a3902b09%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637720661863289918%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D2652Ptojb17Rbe%252FgPVm4G1%252FaUVjsEOkmPS3GaiWfsik%253D%26reserved%3D0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The time of the aparc.stats is 1h and 20min after the modification of the file pial.T2, and in the case of the T1 only processing the time stamp on the apar.stats is 20 min after the modification of the pial.T1. Does this answer your question or should I look into something else? ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu Enviado: martes, 9 de noviembre de 2021 18:09 Para: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Were the stats files regenerated? Check the modification date
On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Yes the pial surface changed and the white did not. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Enviado: martes, 9 de noviembre de 2021 14:49 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
⚠ Caution: External sender
The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1DIYQjcS7A4cLkHlo28KnUgtMLO9nJ3ZDRteABbylq8V276...https://secure-web.cisco.com/1ESUOWHZrRXFPIgr9RyO_RBL6qU2WJniTnZyLkbcxSpTEFZktbgzeB0hPOQROs7K0Mza92hU-GRa-hiXc5IiG04mIPJIydz75Oq-tyRJQ_poRIZs9HS8rrV1hJZX44APslFE2JdAajvqD_0ZzPn0Q-qrLqJ-ZQQl4hz5rNoX5CjX2eqgjDm4fh0NYI5n1TM2z12SFhKojwNJ7sCLEhsTwmCxLws8SNN34znatha_iM_B86d2l0g8nsyxBNQY0UcivT9RiNQpNQCi9tPmiRLzzU9IOEGJKtdsI0tc395AIoOofXqCJmo7Raej0zISczCHR/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F18jwzbq6koFUTgWZ3UTwDDmlFp3S7nENHKQKswzAWRKaGqzqQN1trIM1DDK8KzIrBAkv8mTtDRKWsd80P2yCOv-Np-OmYSj3xiGHzQG2mabATiVM1uPc6PjwXCJ0X-tBXdzlOX7SgZyYYHU6N93WTwOEBar4IZVFPvc01svJzhki4aI1mQ7MrWPozbUlm43LGrEqEaSFLxK35Nk6mMcC0hjQOC11riEW0QECyGC8BHuU4Tkcb-837ldeX4SBiIoCjX_tzoRGCPl3sTxmWx-RE9N1sZsVp4TZWWAohf89L7gtAshZIp54PbgmU8-bwevZV%252Fhttps%25253A%25252F%25252Feur01.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fmail.nmr.mgh.harvard.edu%2525252Fmailman%2525252Flistinfo%2525252Ffreesurfer%252526data%25253D04%2525257C01%2525257Cg.leal%25252540ucl.ac.uk%2525257Cb69c988d010e48c55add08d9a3902b09%2525257C1faf88fea9984c5b93c9210a11d9a5c2%2525257C0%2525257C0%2525257C637720661863289918%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253D2652Ptojb17Rbe%2525252FgPVm4G1%2525252FaUVjsEOkmPS3GaiWfsik%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cg.leal%2540ucl.ac.uk%257C7f6c2d00f0d949ae7c9a08d9a3ac3efc%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637720782469513542%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DgXoQxxEJ1mdHqFPgGe2C2wCrhm6FlG65qmbCIR9Y4f8%253D%26reserved%3D0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1DIYQjcS7A4cLkHlo28KnUgtMLO9nJ3ZDRteABbylq8V276...https://secure-web.cisco.com/1rso-VqdbnZGVwUe6Hxd84fp6rtdOffIqwSYpjAAE9mXUL5D5GPJFDnk35VdzIeLN-3vnZwLGIrcw3i5u9VxTLCm2Bm5Fv0fM04oMBSuHuF1IL9zlmdCKYTL8byRDEnF1M0NErC4EglKGQ5HSIlRmSrmTEr686bjUJrqonksR4iOkEFKhQ2DK1CDGnbQ8K8cu_Mn-8pm8UjEKGdlX7vmAmVinJ1oLOstVy-GDZZx8DnV6p_SqHFAh3Yq5QRLrtGtyWRSzUm_QLKGV-PHFOR9o2cCrNUYvCqZ1dM1fQEfjimkzraavt6PW7SN3fGOps0BG/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cg.leal%2540ucl.ac.uk%257C7f6c2d00f0d949ae7c9a08d9a3ac3efc%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637720782469523504%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3Deow4Mgmh6mv98rhqXjELceHoVUpDXTUdoQgWFF95HiM%253D%26reserved%3D0
In your first post, you said that you were confused as to why the thickness and volume were changing but the surface was not changing. Then you said that the pial surface changed. Does that answer your first question?
On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
The time of the aparc.stats is 1h and 20min after the modification of the file pial.T2, and in the case of the T1 only processing the time stamp on the apar.stats is 20 min after the modification of the pial.T1. Does this answer your question or should I look into something else?
*De:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu *Enviado:* martes, 9 de noviembre de 2021 18:09 *Para:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats Were the stats files regenerated? Check the modification date
On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Yes the pial surface changed and the white did not.
*De:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU *Enviado:* martes, 9 de noviembre de 2021 14:49 *Para:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
⚠ Caution: External sender
The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1ESUOWHZrRXFPIgr9RyO_RBL6qU2WJniTnZyLkbcxSpTEFZktbgzeB0hPOQROs7K0Mza92hU-GRa-hiXc5IiG04mIPJIydz75Oq-tyRJQ_poRIZs9HS8rrV1hJZX44APslFE2JdAajvqD_0ZzPn0Q-qrLqJ-ZQQl4hz5rNoX5CjX2eqgjDm4fh0NYI5n1TM2z12SFhKojwNJ7sCLEhsTwmCxLws8SNN34znatha_iM_B86d2l0g8nsyxBNQY0UcivT9RiNQpNQCi9tPmiRLzzU9IOEGJKtdsI0tc395AIoOofXqCJmo7Raej0zISczCHR/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F18jwzbq6koFUTgWZ3UTwDDmlFp3S7nENHKQKswzAWRKaGqzqQN1trIM1DDK8KzIrBAkv8mTtDRKWsd80P2yCOv-Np-OmYSj3xiGHzQG2mabATiVM1uPc6PjwXCJ0X-tBXdzlOX7SgZyYYHU6N93WTwOEBar4IZVFPvc01svJzhki4aI1mQ7MrWPozbUlm43LGrEqEaSFLxK35Nk6mMcC0hjQOC11riEW0QECyGC8BHuU4Tkcb-837ldeX4SBiIoCjX_tzoRGCPl3sTxmWx-RE9N1sZsVp4TZWWAohf89L7gtAshZIp54PbgmU8-bwevZV%252Fhttps%25253A%25252F%25252Feur01.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fmail.nmr.mgh.harvard.edu%2525252Fmailman%2525252Flistinfo%2525252Ffreesurfer%252526data%25253D04%2525257C01%2525257Cg.leal%25252540ucl.ac.uk%2525257Cb69c988d010e48c55add08d9a3902b09%2525257C1faf88fea9984c5b93c9210a11d9a5c2%2525257C0%2525257C0%2525257C637720661863289918%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253D2652Ptojb17Rbe%2525252FgPVm4G1%2525252FaUVjsEOkmPS3GaiWfsik%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cg.leal%2540ucl.ac.uk%257C7f6c2d00f0d949ae7c9a08d9a3ac3efc%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637720782469513542%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DgXoQxxEJ1mdHqFPgGe2C2wCrhm6FlG65qmbCIR9Y4f8%253D%26reserved%3D0
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Sorry I did not explain myself well. What I mean is that for some regions of the brain this is what happens:
Region
lateralorbitofrontal 2969 2085 5489 2.469
lateralorbitofrontal 2969 2085 5173 2.566
________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu Enviado: martes, 9 de noviembre de 2021 20:13 Para: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
In your first post, you said that you were confused as to why the thickness and volume were changing but the surface was not changing. Then you said that the pial surface changed. Does that answer your first question?
On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
The time of the aparc.stats is 1h and 20min after the modification of the file pial.T2, and in the case of the T1 only processing the time stamp on the apar.stats is 20 min after the modification of the pial.T1. Does this answer your question or should I look into something else? ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Enviado: martes, 9 de noviembre de 2021 18:09 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Were the stats files regenerated? Check the modification date
On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:
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Yes the pial surface changed and the white did not. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Enviado: martes, 9 de noviembre de 2021 14:49 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
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The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
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Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
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Sorry I did not explain myself well. For some regions of the brain this is what happens:
Region Num Vertices Surf Area GrayVol ThickAvg
lateralorbitofrontal 2969 2085 5489 2.469
lateralorbitofrontal 2969 2085 5173 2.566
The first one corresponds to T1 only and the second one to T1 plus T2 processing. The surface measurement is the same (this happens for all regions) however the volume decreases while the thickness increases, which is why I am confused.
PD: the last mail was sent by mistake, sorry for the spam.
Many thanks, Gonzalo. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu Enviado: martes, 9 de noviembre de 2021 20:13 Para: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
In your first post, you said that you were confused as to why the thickness and volume were changing but the surface was not changing. Then you said that the pial surface changed. Does that answer your first question?
On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:
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The time of the aparc.stats is 1h and 20min after the modification of the file pial.T2, and in the case of the T1 only processing the time stamp on the apar.stats is 20 min after the modification of the pial.T1. Does this answer your question or should I look into something else? ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Enviado: martes, 9 de noviembre de 2021 18:09 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Were the stats files regenerated? Check the modification date
On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:
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Yes the pial surface changed and the white did not. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Enviado: martes, 9 de noviembre de 2021 14:49 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
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The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
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Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
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Ah, I see. Can you upload those two subjects using the method below?
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 11/10/2021 9:33 AM, Castro Leal, Gonzalo wrote:
External Email - Use Caution
Sorry I did not explain myself well. For some regions of the brain this is what happens:
Region Num Vertices Surf Area GrayVol ThickAvg lateralorbitofrontal 2969 2085 5489 2.469 lateralorbitofrontal 2969 2085 5173 2.566 The first one corresponds to T1 only and the second one to T1 plus T2 processing. The surface measurement is the same (this happens for all regions) however the volume decreases while the thickness increases, which is why I am confused.
PD: the last mail was sent by mistake, sorry for the spam.
Many thanks, Gonzalo.
*De:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu *Enviado:* martes, 9 de noviembre de 2021 20:13 *Para:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats In your first post, you said that you were confused as to why the thickness and volume were changing but the surface was not changing. Then you said that the pial surface changed. Does that answer your first question?
On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:
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The time of the aparc.stats is 1h and 20min after the modification of the file pial.T2, and in the case of the T1 only processing the time stamp on the apar.stats is 20 min after the modification of the pial.T1. Does this answer your question or should I look into something else?
*De:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Enviado:* martes, 9 de noviembre de 2021 18:09 *Para:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats Were the stats files regenerated? Check the modification date
On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:
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Yes the pial surface changed and the white did not.
*De:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU *Enviado:* martes, 9 de noviembre de 2021 14:49 *Para:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
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The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
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Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
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I have tried, but I get the following error:
local: Gonzalo_ADNI_sub-020S0899_T2.tar.gz remote: Gonzalo_ADNI_sub-020S0899_T2.tar.gz 421 Service not available, remote server has closed connection
________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu Enviado: miércoles, 10 de noviembre de 2021 15:09 Para: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Ah, I see. Can you upload those two subjects using the method below?
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 11/10/2021 9:33 AM, Castro Leal, Gonzalo wrote:
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Sorry I did not explain myself well. For some regions of the brain this is what happens:
Region Num Vertices Surf Area GrayVol ThickAvg
lateralorbitofrontal 2969 2085 5489 2.469
lateralorbitofrontal 2969 2085 5173 2.566
The first one corresponds to T1 only and the second one to T1 plus T2 processing. The surface measurement is the same (this happens for all regions) however the volume decreases while the thickness increases, which is why I am confused.
PD: the last mail was sent by mistake, sorry for the spam.
Many thanks, Gonzalo. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Enviado: martes, 9 de noviembre de 2021 20:13 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
In your first post, you said that you were confused as to why the thickness and volume were changing but the surface was not changing. Then you said that the pial surface changed. Does that answer your first question?
On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:
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The time of the aparc.stats is 1h and 20min after the modification of the file pial.T2, and in the case of the T1 only processing the time stamp on the apar.stats is 20 min after the modification of the pial.T1. Does this answer your question or should I look into something else? ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Enviado: martes, 9 de noviembre de 2021 18:09 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Were the stats files regenerated? Check the modification date
On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:
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Yes the pial surface changed and the white did not. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Enviado: martes, 9 de noviembre de 2021 14:49 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
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The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
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Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
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I looked at your data. The problem is that the T2-pial placement is not very good. In some places it is much thinner, in some places it it somewhat thicker. This makes the volume computation a little unpredictable (can't just assume that average thickenss*area will give you a reasonable value). The T2-pial is not placed well because the T2 is very low resolution (3mm slice thickness); it is hard to determine the boundaries of a 2-3mm structure when your slices are 3mm
On 11/10/2021 10:55 AM, Castro Leal, Gonzalo wrote:
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I have tried, but I get the following error:
local: Gonzalo_ADNI_sub-020S0899_T2.tar.gz remote: Gonzalo_ADNI_sub-020S0899_T2.tar.gz 421 Service not available, remote server has closed connection
*De:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu *Enviado:* miércoles, 10 de noviembre de 2021 15:09 *Para:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats Ah, I see. Can you upload those two subjects using the method below?
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 11/10/2021 9:33 AM, Castro Leal, Gonzalo wrote:
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Sorry I did not explain myself well. For some regions of the brain this is what happens:
Region Num Vertices Surf Area GrayVol ThickAvg lateralorbitofrontal 2969 2085 5489 2.469 lateralorbitofrontal 2969 2085 5173 2.566 The first one corresponds to T1 only and the second one to T1 plus T2 processing. The surface measurement is the same (this happens for all regions) however the volume decreases while the thickness increases, which is why I am confused.
PD: the last mail was sent by mistake, sorry for the spam.
Many thanks, Gonzalo.
*De:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Enviado:* martes, 9 de noviembre de 2021 20:13 *Para:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats In your first post, you said that you were confused as to why the thickness and volume were changing but the surface was not changing. Then you said that the pial surface changed. Does that answer your first question?
On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:
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The time of the aparc.stats is 1h and 20min after the modification of the file pial.T2, and in the case of the T1 only processing the time stamp on the apar.stats is 20 min after the modification of the pial.T1. Does this answer your question or should I look into something else?
*De:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Enviado:* martes, 9 de noviembre de 2021 18:09 *Para:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats Were the stats files regenerated? Check the modification date
On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:
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Yes the pial surface changed and the white did not.
*De:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU *Enviado:* martes, 9 de noviembre de 2021 14:49 *Para:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
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The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
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Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
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Thanks for the effort. I assumed that since this was data was from a study, it could be used in Freesurfer. Good to know from now on.
Many thanks, Gonzalo. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edu Enviado: jueves, 11 de noviembre de 2021 20:25 Para: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
I looked at your data. The problem is that the T2-pial placement is not very good. In some places it is much thinner, in some places it it somewhat thicker. This makes the volume computation a little unpredictable (can't just assume that average thickenss*area will give you a reasonable value). The T2-pial is not placed well because the T2 is very low resolution (3mm slice thickness); it is hard to determine the boundaries of a 2-3mm structure when your slices are 3mm
On 11/10/2021 10:55 AM, Castro Leal, Gonzalo wrote:
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I have tried, but I get the following error:
local: Gonzalo_ADNI_sub-020S0899_T2.tar.gz remote: Gonzalo_ADNI_sub-020S0899_T2.tar.gz 421 Service not available, remote server has closed connection
________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Enviado: miércoles, 10 de noviembre de 2021 15:09 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Ah, I see. Can you upload those two subjects using the method below?
From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 11/10/2021 9:33 AM, Castro Leal, Gonzalo wrote:
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Sorry I did not explain myself well. For some regions of the brain this is what happens:
Region Num Vertices Surf Area GrayVol ThickAvg
lateralorbitofrontal 2969 2085 5489 2.469
lateralorbitofrontal 2969 2085 5173 2.566
The first one corresponds to T1 only and the second one to T1 plus T2 processing. The surface measurement is the same (this happens for all regions) however the volume decreases while the thickness increases, which is why I am confused.
PD: the last mail was sent by mistake, sorry for the spam.
Many thanks, Gonzalo. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Enviado: martes, 9 de noviembre de 2021 20:13 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
In your first post, you said that you were confused as to why the thickness and volume were changing but the surface was not changing. Then you said that the pial surface changed. Does that answer your first question?
On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:
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The time of the aparc.stats is 1h and 20min after the modification of the file pial.T2, and in the case of the T1 only processing the time stamp on the apar.stats is 20 min after the modification of the pial.T1. Does this answer your question or should I look into something else? ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Enviado: martes, 9 de noviembre de 2021 18:09 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Were the stats files regenerated? Check the modification date
On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:
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Yes the pial surface changed and the white did not. ________________________________ De: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu en nombre de Douglas N. Greve dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU Enviado: martes, 9 de noviembre de 2021 14:49 Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
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The white surface won't change, but the pial surface should change. Can you verify that the pial surface changed?
On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:
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Hello,
I wanted to compare the results of the aparc.stats on the same subjects when only the T1 is used and when T2 is used for pial refinement along with the same T1. To my surprise the tickness increased (on average across regions), the gm volume decreased and the surface didnt change. My questions is how is that the thickness increased and the volume decresed if the surface did not change? (I used freesrufer 7.1.1)
Many thanks, Gonzalo.
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pk4QplKq08RBB2eaDUl3CiDopizsT5Zm-raVo3hr4c339B...https://secure-web.cisco.com/1mZ7f39qZCKpW-is6dGunR0TIU0qJ71X1zorLa7Ut4ZbIDzMK9WpByyglr0y3CsIWPVwUniAkl73Kev5iUVpTot97vF3JSlPMvg_7rufCQ6X4lQysvV63avNUILpm8leWw8QjDcsX0BcLiag-DU8VUQpbuJpHMIJr4LG1n_eIO6VoLOqRSrIqGadptGAvnhFUDK-2w9zirR6VUDmb9JORd9w9XxzelVb_69V0PfvZQ2iJmi1dLzg6fbZRFwPKDxAzIMRa1ITxUvzS_aeKKbzpBQ/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1uXrFuCSzp69-VDRZAdXyp4_TLKv0dJ6T2S_hXC9pfNpBJ0yuWVl9SDBvP2t1V744OO7zvPJp1ssxUGw01uiarrgjoqDO6p8LgOVgv2I8TJwYdsMl5hCDnZCfZtq33fvsQw0SvssBaJqhyYlx3K8kN232ZgAG9JaongMQQKFDxS8IVvL2njGIFwyVivRBUgPpsjbD84p0gvUhR0DvQIbVRAYYPWmhar4GnKoFT8K8jt-_iPAWZlTGSE-ubxTJDLTmDh9J_92MOQ5SnfhRlFBgUg%252Fhttps%25253A%25252F%25252Feur01.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1wWtJ4fPdKkKN80o4LAwR0fIZ1qaoa4YmfqwEBcyI1ozjle6na28ge-I3gQmWq6liOVGY36RCpp03So-Awu7vW7uyYCdYN02nIGCUMMNPEA7go7eSlB1TzXbxg3ZSJzxPgnj7P0K9GK1xCl3R-nd9oc2tqGTQFDL34-hLOVW5oecd2C_WcU3oN17dRTvUx_KKH41kFO-WZ7Vv82AwGh97G7cVIMp-zCevppF7NXTywt9OifvrhfXJ6LgvkaKevJxhFwCnH5aZ9xeXTnep7Sg6IWGUOi_eKGfqIVFnUr7R2BZC_PHYoxLFV4iB_e7zXkpi%2525252Fhttps%252525253A%252525252F%252525252Feur01.safelinks.protection.outlook.com%252525252F%252525253Furl%252525253Dhttps%25252525253A%25252525252F%25252525252Fsecure-web.cisco.com%25252525252F1rso-VqdbnZGVwUe6Hxd84fp6rtdOffIqwSYpjAAE9mXUL5D5GPJFDnk35VdzIeLN-3vnZwLGIrcw3i5u9VxTLCm2Bm5Fv0fM04oMBSuHuF1IL9zlmdCKYTL8byRDEnF1M0NErC4EglKGQ5HSIlRmSrmTEr686bjUJrqonksR4iOkEFKhQ2DK1CDGnbQ8K8cu_Mn-8pm8UjEKGdlX7vmAmVinJ1oLOstVy-GDZZx8DnV6p_SqHFAh3Yq5QRLrtGtyWRSzUm_QLKGV-PHFOR9o2cCrNUYvCqZ1dM1fQEfjimkzraavt6PW7SN3fGOps0BG%25252525252Fhttps%2525252525253A%2525252525252F%2525252525252Feur01.safelinks.protection.outlook.com%2525252525252F%2525252525253Furl%2525252525253Dhttps%252525252525253A%252525252525252F%252525252525252Fmail.nmr.mgh.harvard.edu%252525252525252Fmailman%252525252525252Flistinfo%252525252525252Ffreesurfer%25252525252526data%2525252525253D04%252525252525257C01%252525252525257Cg.leal%2525252525252540ucl.ac.uk%252525252525257C7f6c2d00f0d949ae7c9a08d9a3ac3efc%252525252525257C1faf88fea9984c5b93c9210a11d9a5c2%252525252525257C0%252525252525257C0%252525252525257C637720782469523504%252525252525257CUnknown%252525252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%252525252525253D%252525252525257C1000%25252525252526sdata%2525252525253Deow4Mgmh6mv98rhqXjELceHoVUpDXTUdoQgWFF95HiM%252525252525253D%25252525252526reserved%2525252525253D0%2525252526data%252525253D04%25252525257C01%25252525257Cg.leal%252525252540ucl.ac.uk%25252525257Cf733c66804b046329a5708d9a3bda5a6%25252525257C1faf88fea9984c5b93c9210a11d9a5c2%25252525257C0%25252525257C0%25252525257C637720857213279868%25252525257CUnknown%25252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%25252525253D%25252525257C1000%2525252526sdata%252525253DZ%25252525252B4HXSoVx0sKpYp9y0kzqznFQU6%25252525252Bk%25252525252FgsCjDidj3Cs9Q%25252525253D%2525252526reserved%252525253D0%252526data%25253D04%2525257C01%2525257Cg.leal%25252540ucl.ac.uk%2525257C38f7972875ec4345ec9d08d9a45cecbe%2525257C1faf88fea9984c5b93c9210a11d9a5c2%2525257C0%2525257C0%2525257C637721541288542743%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DFtzDEWAFKjx4GA1ntSRj1sGaqVCOcfCPby1JG8sd388%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cg.leal%2540ucl.ac.uk%257C2666cc7a164f427bca2308d9a551d13c%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637722593094552518%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DLKiV5y0vOkh3Bw8pvfMvWA9ffFVTRdswu3oETfKfI6A%253D%26reserved%3D0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pk4QplKq08RBB2eaDUl3CiDopizsT5Zm-raVo3hr4c339B...https://secure-web.cisco.com/1c7iuHdRtGIzYQwix3ThheVAY9DzTkGWYJZlpN47hEOg6cUdFChNRavJcyaSHv6jG8fFYzmxVrF6QxlKF58KVwQqX5OhcWdTJwGd3AVAm_Xng-rKw6zsMKh2zo5JMYKEEhl5Z0K9jjB5RCOr37b9_BsZ4cFvv-JKzpiEx8tIsKvFWLJK7GD05xclXVVaW4DL2vGJPcAw4PuTHgr8Z0BCU_zhFVQVYWEwv6L8cLE-bcSuOwAMpX5I_O97LTvIej8nWKX7IxKasYO9wS_ctkimLzQ/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1b3i7_IKDlklhZOc8jt353e2EmIskRe2JLF7wxcIbrsroZiT4fEuEye9B7eWYnqlYYaUkSMDy4QQ6hsaZ_Rm7NQ8XKU3g-UcH-fLq4CtCivvtdokurDZG7aqy2TWPZ0JoUiwgmb4FrKub_b37Jj1y-d2CEE0AypFM8FUAgvt2jk9r-l1UIMy0MP68vazNQsCz-g09i3-p43_Bjcrkc5li4510-wMjs5BdZQm7Gh_y3D6qoPMvbheKfpBvJOQ1k5_MRlkqQzKn22_eoMkSlC9rGbKYUp9oLxCIRAAyvDja4XQihTB2qDxBpubduuMpI4AXC8K1b-FwYbwkTBZ8ckCcZA%252Fhttps%25253A%25252F%25252Feur01.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1dqeQ_oJNd-J6PAjhBPEIyOMw89mGtulod96SqbP9XqjIs_EULs4DdTT_jbRzByT-e4S931EsseqlxSvgnHUwUm_ByK2ZqAkHs4VppIdXloRDycPD52GdMoRPIhqtOz5ZZlcNL5UZszeCpbR2nQDpB70_UFLXInHhtuJvsO8I7dqkVKOzQ_GVOgIVfA4ylsTCq5LFoFJyiLS3txwb0GEHjEQhdfeVkxejFt_7yYPXuxLHYxCiE629HHhA1idQQB5o7JdkMCzGVvePJacbGCAMURT3iAdUSnOff0cPMFF0wDbF189Nd4G9h999a-TCdXcU%2525252Fhttps%252525253A%252525252F%252525252Feur01.safelinks.protection.outlook.com%252525252F%252525253Furl%252525253Dhttps%25252525253A%25252525252F%25252525252Fmail.nmr.mgh.harvard.edu%25252525252Fmailman%25252525252Flistinfo%25252525252Ffreesurfer%2525252526data%252525253D04%25252525257C01%25252525257Cg.leal%252525252540ucl.ac.uk%25252525257Cf733c66804b046329a5708d9a3bda5a6%25252525257C1faf88fea9984c5b93c9210a11d9a5c2%25252525257C0%25252525257C0%25252525257C637720857213289825%25252525257CUnknown%25252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%25252525253D%25252525257C1000%2525252526sdata%252525253DMvqG4tScBH4fvh50UUd55jviCX76Gq529oILy5Q0stI%25252525253D%2525252526reserved%252525253D0%252526data%25253D04%2525257C01%2525257Cg.leal%25252540ucl.ac.uk%2525257C38f7972875ec4345ec9d08d9a45cecbe%2525257C1faf88fea9984c5b93c9210a11d9a5c2%2525257C0%2525257C0%2525257C637721541288552693%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DBejFNtYbpYW0aJOa2UZOTL9vGGOZ%2525252B2oLX%2525252B3D4nnHSwg%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cg.leal%2540ucl.ac.uk%257C2666cc7a164f427bca2308d9a551d13c%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637722593094562472%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D%252FLl%252BadY2zumdUmsIeRk%252F3ctEhN4nhKQI3OmUAjeykPc%253D%26reserved%3D0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pk4QplKq08RBB2eaDUl3CiDopizsT5Zm-raVo3hr4c339B...https://secure-web.cisco.com/18Ha-A4finrAU1ao6KSSO0o_lWqTIBGVxzXTcNMM2oZTgxk8NaeAxn346d4vQJy7mCx1T5RCPW1tv5Urx42TbxCoSrlE-QErljQj8-CFy2mNKrEHqxWed_0ahKSF4TbVIaxvtajadFCvLhN9K7hLlCp0Ss6zvrhYvitbOmB6mL2uol8SX1wDSTqfcgvvJgoQVwIp9h1NPMj60c3up-6-CjhoHwDL9J2v0NFe6soitVvToQMk2gTWJI5jIXx1WlZr4ayNyoP14J6EXP4Yk5L7IMDE93x0RguGbwxez-o7jKBb2uusi3YoSl1rZ5LapuEmc/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1H1sFJEjC4AzrDp2q0Biszw9atBPV14ErTzurYpg4tVJFjnoXYjvTLZo3iMZA8FNlrQIecuyniHy_OnJLSHvFIsRLUOhTbPFrUaaw9hB_6_zJWudk6AwEpQi0MMd1mH7sbugdkn2uc2WAtTOvGuFIqOjL0T_CUOvLz23ii8AcacgnAIsKd8RhNO4OgIttLRaAkZ_8bz_NUlUITAWs-ssNfIsR3lH82FP3DHf5TwiCfpuNYgFITGZD5fuAtg2jxWcV7q-IyswGVWLfgsPOFAPTHdS-g1Ovv4gnVxuno9DtxbFj0le6Sd_zHa7SGjs8DSV5bvowhI2kcolKoyfTgyfy0g%252Fhttps%25253A%25252F%25252Feur01.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fmail.nmr.mgh.harvard.edu%2525252Fmailman%2525252Flistinfo%2525252Ffreesurfer%252526data%25253D04%2525257C01%2525257Cg.leal%25252540ucl.ac.uk%2525257C38f7972875ec4345ec9d08d9a45cecbe%2525257C1faf88fea9984c5b93c9210a11d9a5c2%2525257C0%2525257C0%2525257C637721541288562661%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C1000%252526sdata%25253DO1McAo1fysTtJg1NmiJz22TcKBtV0%2525252F73Ggxw0vgjPkM%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Cg.leal%2540ucl.ac.uk%257C2666cc7a164f427bca2308d9a551d13c%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637722593094562472%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DNToNLjhJ6jTgq3YCAzbpoyS6LiaGZuuUvpC3jP9QiVw%253D%26reserved%3D0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1pk4QplKq08RBB2eaDUl3CiDopizsT5Zm-raVo3hr4c339B...https://secure-web.cisco.com/1RMbUlElwTeRtbLpYnOgWP2hSQm4k00GmN9_3hFbl1OJe2UPxFutH5X_5oNdNwdAE6IXZXbvP3aoYbnC5hR1xuGW2P-B0J9xsoQFA6K1nJj8o5JiuEXDqO_YZ6KY3wLBDsB8NyrFJotygAPSnayOB2B_yau90tC_OiBlE7pS3gC1pbHkKwde8J_NWELlImVi7Gu2K9xcZ2oX6Kp76xDL3Z0IaxA3eEBT9dJqN3o4NwabZ7AkhH3v-0rlMu9I0nvf570_vYT7JRlou10k87XGBfoN_Tv7kP01l-EJgiIWJZel3lFcSwYq2je40JJ2A-Uw5/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Cg.leal%2540ucl.ac.uk%257C2666cc7a164f427bca2308d9a551d13c%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C637722593094572437%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D5yAxLoo9UWNy5NqStHO4eH%252BnEVo9H9R%252BCviZ6VfRJlM%253D%26reserved%3D0
freesurfer@nmr.mgh.harvard.edu
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Castro Leal, Gonzalo -
Douglas N. Greve