External Email - Use Caution
Dear Freesurfer Developers,
I am currently running the Longitudinal Pipeline on a cohort with significant portions of brain tissue removed. The obtained base templates overall look reasonable, however, when overlaying the transformed session T1ws and flicking between them, there still are noticeable residual differences. This is not surprising, given the inevitable brain shift after tissue removal, which rigid registration cannot account for. In my search for a non-linear base template option I came across the "Longitudinal FreeSurfer with non-linear subject-specific template improves sensitivity to cortical thinning” ISMRM abstract (https://secure-web.cisco.com/1me4RY0enlek75e3PAqIseSGOO7tfF84eBwPlWXYndHKO5G...) as well as related code on Github (https://secure-web.cisco.com/10WRpCPnvc4D9H2TOaZHsTUn0u7cWtVKoReU9EtexFnzvs4...).
I was wondering whether you could provide insights into what you think the best strategy for obtaining reliable longitudinal cortical thickness measurements in such a dataset. Do you have a feel for whether the Longitudinal Freesurfer processing stream still provides benefits over Cross-Sectional analysis in the presence of large defects? Would you recommend giving the above-mentioned non-linear implementation a shot or were there other reasons the feature has not been implemented yet in the official version?
Thanks already in advance!
Best
Philip
Hi Philip,
The deformable template was most beneficial when differences between time points (TPs) were largest. While this is perhaps not surprising, it meant that the long registration time of 8h/TP in the abstract was not time well spent since we were already certain of group differences.
We generally recommend the longitudinal stream for longitudinal data since much information is shared between the TPs. The median rigid template is typically a robust starting point for the processing of the individual TPs, sometimes even for developmental studies where you see the size of the brain increase.
In your specific case, non-linear registration (using an image-intensity objective like in the abstract) might be detrimental. The algorithm will likely move tissue from outside the resected area into this area since the scan before resection will have matching intensities there, but this won’t necessarily make for a good template.
Malte
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Philip P philip.pruckner@gmail.com Sent: Sunday, February 4, 2024 01:48 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects
External Email - Use Caution
Dear Freesurfer Developers,
I am currently running the Longitudinal Pipeline on a cohort with significant portions of brain tissue removed. The obtained base templates overall look reasonable, however, when overlaying the transformed session T1ws and flicking between them, there still are noticeable residual differences. This is not surprising, given the inevitable brain shift after tissue removal, which rigid registration cannot account for. In my search for a non-linear base template option I came across the "Longitudinal FreeSurfer with non-linear subject-specific template improves sensitivity to cortical thinning” ISMRM abstract (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://archive.ismrm.org/2020/1050.htmlhttps://secure-web.cisco.com/1me4RY0enlek75e3PAqIseSGOO7tfF84eBwPlWXYndHKO5G2tJADVy-TNvBizJR-LC2_sMvVChG7l5Pa8fM2tIAiP3DQT-SSQTQqRMUoLjOtjqu6MziPDQmMNRY5acq-T2Ufgp-DfTUhXPmCjLOm0i9Su5AxbRJ9lgN0NROMe0D3NZQJ0s72k_2YyzwWh9hncuI8MPyo0OJm0D5IdIvd_8-X2QAvcS54AE_ctHqeQi5RdtlySv2EfrrbKcuNkH5npl63jHoUptIM9QgGYk0XMO4RsHZYRXlfQW1IXJ1n62rfuX8xXiSbcBFppSYPx0utW1SkV7zhUcfnHb0qhtJwUFw/https%3A%2F%2Farchive.ismrm.org%2F2020%2F1050.html) as well as related code on Github (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/mu40/freesurfer/tree/nf-long-nonlinhttps://secure-web.cisco.com/10WRpCPnvc4D9H2TOaZHsTUn0u7cWtVKoReU9EtexFnzvs4ApXqcGX5LXIAqA1gw_jDyZM0n74IRnrQrlh-uC5HiUAB3QqdEQ4zL9c8zhF_OLGSzGLytRBv-qE6DlzxoJtfknjZSMHEk9AVKlDkNKUwBjYFIOBfFv0DA9Yeb5gqDUcqqZAprEL025Pp2xpCpTM3ZS5Qm_zuM2FG1j0boLUTmrLOeHCk3ls6LB6hI03mwTM2feKe8q6B2xiqJvcLmC8dKpj0jL8EEzZNi8PpkbFflk3RYfghezpSY7yOXY-dgVEzNbcZOVNd4lNmn-aZBLK1zqNqtODLsPG0JOP_Q3wA/https%3A%2F%2Fgithub.com%2Fmu40%2Ffreesurfer%2Ftree%2Fnf-long-nonlin).
I was wondering whether you could provide insights into what you think the best strategy for obtaining reliable longitudinal cortical thickness measurements in such a dataset. Do you have a feel for whether the Longitudinal Freesurfer processing stream still provides benefits over Cross-Sectional analysis in the presence of large defects? Would you recommend giving the above-mentioned non-linear implementation a shot or were there other reasons the feature has not been implemented yet in the official version?
Thanks already in advance!
Best
Philip
External Email - Use Caution
Hi Malte,
Thanks for the response, it’s encouraging to hear you think the longitudinal pipeline will still provide benefits, even in the absence of a non-linear template!
However out of interest: I was able to generate a non-linear unbiased session template without moving tissue from outside into the resection area. If I’d want to use this template for the analysis, is there any modifications I’d have to make to the existing workflow except for 1) using the non-linear template as norm_template.mgz and 2) running all commands that make use of the session_to_template.lta transforms with the appropriate non-linear warps?
Thanks for your help, its greatly appreciated !
Best, Philip
On 27.02.2024, at 08:42, Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu wrote:
Hi Philip,
The deformable template was most beneficial when differences between time points (TPs) were largest. While this is perhaps not surprising, it meant that the long registration time of 8h/TP in the abstract was not time well spent since we were already certain of group differences.
We generally recommend the longitudinal stream for longitudinal data since much information is shared between the TPs. The median rigid template is typically a robust starting point for the processing of the individual TPs, sometimes even for developmental studies where you see the size of the brain increase.
In your specific case, non-linear registration (using an image-intensity objective like in the abstract) might be detrimental. The algorithm will likely move tissue from outside the resected area into this area since the scan before resection will have matching intensities there, but this won’t necessarily make for a good template.
Malte
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Philip P philip.pruckner@gmail.com Sent: Sunday, February 4, 2024 01:48 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects
External Email - Use CautionDear Freesurfer Developers,
I am currently running the Longitudinal Pipeline on a cohort with significant portions of brain tissue removed. The obtained base templates overall look reasonable, however, when overlaying the transformed session T1ws and flicking between them, there still are noticeable residual differences. This is not surprising, given the inevitable brain shift after tissue removal, which rigid registration cannot account for. In my search for a non-linear base template option I came across the "Longitudinal FreeSurfer with non-linear subject-specific template improves sensitivity to cortical thinning” ISMRM abstract (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/17N_xqg9IuaXhy0eeSRmExNHOVIHuG1VhD7ehDfM9lhAHQx...https://secure-web.cisco.com/1me4RY0enlek75e3PAqIseSGOO7tfF84eBwPlWXYndHKO5G2tJADVy-TNvBizJR-LC2_sMvVChG7l5Pa8fM2tIAiP3DQT-SSQTQqRMUoLjOtjqu6MziPDQmMNRY5acq-T2Ufgp-DfTUhXPmCjLOm0i9Su5AxbRJ9lgN0NROMe0D3NZQJ0s72k_2YyzwWh9hncuI8MPyo0OJm0D5IdIvd_8-X2QAvcS54AE_ctHqeQi5RdtlySv2EfrrbKcuNkH5npl63jHoUptIM9QgGYk0XMO4RsHZYRXlfQW1IXJ1n62rfuX8xXiSbcBFppSYPx0utW1SkV7zhUcfnHb0qhtJwUFw/https%3A%2F%2Farchive.ismrm.org%2F2020%2F1050.html) as well as related code on Github (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1kHilcnCgkwQrldX6iuJ88RE0UoXG5EVoDzuvrFNtUvMJmI...
AnZeds3EIeBhQ/https%3A%2F%2Fgithub.com%2Fmu40%2Ffreesurfer%2Ftree%2Fnf-long-nonlinhttps://secure-web.cisco.com/10WRpCPnvc4D9H2TOaZHsTUn0u7cWtVKoReU9EtexFnzvs4ApXqcGX5LXIAqA1gw_jDyZM0n74IRnrQrlh-uC5HiUAB3QqdEQ4zL9c8zhF_OLGSzGLytRBv-qE6DlzxoJtfknjZSMHEk9AVKlDkNKUwBjYFIOBfFv0DA9Yeb5gqDUcqqZAprEL025Pp2xpCpTM3ZS5Qm_zuM2FG1j0boLUTmrLOeHCk3ls6LB6hI03mwTM2feKe8q6B2xiqJvcLmC8dKpj0jL8EEzZNi8PpkbFflk3RYfghezpSY7yOXY-dgVEzNbcZOVNd4lNmn-aZBLK1zqNqtODLsPG0JOP_Q3wA/https%3A%2F%2Fgithub.com%2Fmu40%2Ffreesurfer%2Ftree%2Fnf-long-nonlin).
I was wondering whether you could provide insights into what you think the best strategy for obtaining reliable longitudinal cortical thickness measurements in such a dataset. Do you have a feel for whether the Longitudinal Freesurfer processing stream still provides benefits over Cross-Sectional analysis in the presence of large defects? Would you recommend giving the above-mentioned non-linear implementation a shot or were there other reasons the feature has not been implemented yet in the official version?
Thanks already in advance!
Best
Philip The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1rl2yFKAdl2Y2_4nr-RVTrY1c4EFuD0xPFxP3boCfk5ckrz... https://secure-web.cisco.com/1rl2yFKAdl2Y2_4nr-RVTrY1c4EFuD0xPFxP3boCfk5ckrz4Wqon96BXir1VgKFXAkhJ9SQfeUf-ltuBeE6NhEzFCnsPIRKYZeRLaXsk58nLN1VMZ9mKUQQ5vKPKyo5Rn5UogTC60qloAHgbgTriDHQoCGMcyT2RMSSMy8heYVUy13leFd-42cVwJsKtZVWJN-OUl-J1QdbGwNd0KkOiAT1MxqBiWAAOGBvMeSn2MQ5SV8BC6Cu9BkCDwlYn-6VItrVXIljiwRsbQ83X6s0hZkOb82gtn1vgx_9w1LEM_bOwXwO8dqI5Ze6ztZQShcrmZY3CY8K99haq22-tIO6sRtA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
If you construct the non-linear template within the current rigid (or affine) mid-space, then there are two things you can do.
(1) You can just replace the base image and run the remainder of the base and longitudinal streams as is to transfer the results out to the TPs using the rigid (or affine) LTAs. This is what we did in the abstract, showing improvements with a better-quality base image that can lead to better longitudinal initialization.
(2) On top of this, you can use the warps to initialize the longitudinal TPs as you suggest. Unfortunately, we found that this does not always improve things. For example, volumetric warps are often not that great around the cortex, and initializing the longitudinal surfaces with warps instead of the LTAs turned out to be detrimental when I looked into this.
In principle, we adapted the steps of the longitudinal stream to accept warps but it’s been several years and I’ve not kept track of changes. If you’re up for the challenge, mri_warp_convert --outmgzwarp/--outm3z can be helpful depending on how you estimate your warps.
________________________________________ From: Philip P philip.pruckner@gmail.com Sent: Wednesday, February 28, 2024 20:41 To: Hoffmann, Malte,PhD Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects
External Email - Use Caution
Hi Malte,
Thanks for the response, it’s encouraging to hear you think the longitudinal pipeline will still provide benefits, even in the absence of a non-linear template!
However out of interest: I was able to generate a non-linear unbiased session template without moving tissue from outside into the resection area. If I’d want to use this template for the analysis, is there any modifications I’d have to make to the existing workflow except for 1) using the non-linear template as norm_template.mgz and 2) running all commands that make use of the session_to_template.lta transforms with the appropriate non-linear warps?
Thanks for your help, its greatly appreciated !
Best, Philip
On 27.02.2024, at 08:42, Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu wrote:
Hi Philip,
The deformable template was most beneficial when differences between time points (TPs) were largest. While this is perhaps not surprising, it meant that the long registration time of 8h/TP in the abstract was not time well spent since we were already certain of group differences.
We generally recommend the longitudinal stream for longitudinal data since much information is shared between the TPs. The median rigid template is typically a robust starting point for the processing of the individual TPs, sometimes even for developmental studies where you see the size of the brain increase.
In your specific case, non-linear registration (using an image-intensity objective like in the abstract) might be detrimental. The algorithm will likely move tissue from outside the resected area into this area since the scan before resection will have matching intensities there, but this won’t necessarily make for a good template.
Malte
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Philip P philip.pruckner@gmail.com Sent: Sunday, February 4, 2024 01:48 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects
External Email - Use CautionDear Freesurfer Developers,
I am currently running the Longitudinal Pipeline on a cohort with significant portions of brain tissue removed. The obtained base templates overall look reasonable, however, when overlaying the transformed session T1ws and flicking between them, there still are noticeable residual differences. This is not surprising, given the inevitable brain shift after tissue removal, which rigid registration cannot account for. In my search for a non-linear base template option I came across the "Longitudinal FreeSurfer with non-linear subject-specific template improves sensitivity to cortical thinning” ISMRM abstract (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1bhEHVI_wdXl_mLwpwWSqHCKW0qpfVsSGTa6OP2rDyN8h_S...https://secure-web.cisco.com/1me4RY0enlek75e3PAqIseSGOO7tfF84eBwPlWXYndHKO5G2tJADVy-TNvBizJR-LC2_sMvVChG7l5Pa8fM2tIAiP3DQT-SSQTQqRMUoLjOtjqu6MziPDQmMNRY5acq-T2Ufgp-DfTUhXPmCjLOm0i9Su5AxbRJ9lgN0NROMe0D3NZQJ0s72k_2YyzwWh9hncuI8MPyo0OJm0D5IdIvd_8-X2QAvcS54AE_ctHqeQi5RdtlySv2EfrrbKcuNkH5npl63jHoUptIM9QgGYk0XMO4RsHZYRXlfQW1IXJ1n62rfuX8xXiSbcBFppSYPx0utW1SkV7zhUcfnHb0qhtJwUFw/https%3A%2F%2Farchive.ismrm.org%2F2020%2F1050.html) as well as related code on Github (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pmfGJ-rEOTUEdebbVReP2FLewbwtarzsq0OiG8ICt0vhxO...https://secure-web.cisco.com/10WRpCPnvc4D9H2TOaZHsTUn0u7cWtVKoReU9EtexFnzvs4ApXqcGX5LXIAqA1gw_jDyZM0n74IRnrQrlh-uC5HiUAB3QqdEQ4zL9c8zhF_OLGSzGLytRBv-qE6DlzxoJtfknjZSMHEk9AVKlDkNKUwBjYFIOBfFv0DA9Yeb5gqDUcqqZAprEL025Pp2xpCpTM3ZS5Qm_zuM2FG1j0boLUTmrLOeHCk3ls6LB6hI03mwTM2feKe8q6B2xiqJvcLmC8dKpj0jL8EEzZNi8PpkbFflk3RYfghezpSY7yOXY-dgVEzNbcZOVNd4lNmn-aZBLK1zqNqtODLsPG0JOP_Q3wA/https%3A%2F%2Fgithub.com%2Fmu40%2Ffreesurfer%2Ftree%2Fnf-long-nonlin).
I was wondering whether you could provide insights into what you think the best strategy for obtaining reliable longitudinal cortical thickness measurements in such a dataset. Do you have a feel for whether the Longitudinal Freesurfer processing stream still provides benefits over Cross-Sectional analysis in the presence of large defects? Would you recommend giving the above-mentioned non-linear implementation a shot or were there other reasons the feature has not been implemented yet in the official version?
Thanks already in advance!
Best
Philip The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1wwv94s7JtpES2h6FAik4D5_2xCE945ev4VBoQNeiMICUNf... https://secure-web.cisco.com/1wwv94s7JtpES2h6FAik4D5_2xCE945ev4VBoQNeiMICUNfHxHVu_Hgt9MMUjiScnMVVGOZRK2UofFIB5uRtcOygbZyPJZ41HTj4xiRoijjVUcZvqhY781I8N-V2zpKN8126yStXG1PZvsqkbw-xtX-Eml0RrWlFhQeZNZvtHwafHMnck4fBpVxg9KuM-QYbDpnb5_Uv61Xqfs-2rK20kSywnH8VWhg3cbXSJatqIDw6yDniH4O2cfhnYcRJJGlpVf77n5cieQJ-MmvkUzbTSCX9AULELvWxFQakNkoaiuNAmmfoOUlA_8Td4cEy-XGxV/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
External Email - Use Caution
Thanks Malte, that is very helpful !
On 01.03.2024, at 08:20, Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu wrote:
If you construct the non-linear template within the current rigid (or affine) mid-space, then there are two things you can do.
(1) You can just replace the base image and run the remainder of the base and longitudinal streams as is to transfer the results out to the TPs using the rigid (or affine) LTAs. This is what we did in the abstract, showing improvements with a better-quality base image that can lead to better longitudinal initialization.
(2) On top of this, you can use the warps to initialize the longitudinal TPs as you suggest. Unfortunately, we found that this does not always improve things. For example, volumetric warps are often not that great around the cortex, and initializing the longitudinal surfaces with warps instead of the LTAs turned out to be detrimental when I looked into this.
In principle, we adapted the steps of the longitudinal stream to accept warps but it’s been several years and I’ve not kept track of changes. If you’re up for the challenge, mri_warp_convert --outmgzwarp/--outm3z can be helpful depending on how you estimate your warps.
From: Philip P <philip.pruckner@gmail.com mailto:philip.pruckner@gmail.com> Sent: Wednesday, February 28, 2024 20:41 To: Hoffmann, Malte,PhD Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects
External Email - Use CautionHi Malte,
Thanks for the response, it’s encouraging to hear you think the longitudinal pipeline will still provide benefits, even in the absence of a non-linear template!
However out of interest: I was able to generate a non-linear unbiased session template without moving tissue from outside into the resection area. If I’d want to use this template for the analysis, is there any modifications I’d have to make to the existing workflow except for 1) using the non-linear template as norm_template.mgz and 2) running all commands that make use of the session_to_template.lta transforms with the appropriate non-linear warps?
Thanks for your help, its greatly appreciated !
Best, Philip
On 27.02.2024, at 08:42, Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu wrote:
Hi Philip,
The deformable template was most beneficial when differences between time points (TPs) were largest. While this is perhaps not surprising, it meant that the long registration time of 8h/TP in the abstract was not time well spent since we were already certain of group differences.
We generally recommend the longitudinal stream for longitudinal data since much information is shared between the TPs. The median rigid template is typically a robust starting point for the processing of the individual TPs, sometimes even for developmental studies where you see the size of the brain increase.
In your specific case, non-linear registration (using an image-intensity objective like in the abstract) might be detrimental. The algorithm will likely move tissue from outside the resected area into this area since the scan before resection will have matching intensities there, but this won’t necessarily make for a good template.
Malte
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Philip P philip.pruckner@gmail.com Sent: Sunday, February 4, 2024 01:48 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects
External Email - Use CautionDear Freesurfer Developers,
I am currently running the Longitudinal Pipeline on a cohort with significant portions of brain tissue removed. The obtained base templates overall look reasonable, however, when overlaying the transformed session T1ws and flicking between them, there still are noticeable residual differences. This is not surprising, given the inevitable brain shift after tissue removal, which rigid registration cannot account for. In my search for a non-linear base template option I came across the "Longitudinal FreeSurfer with non-linear subject-specific template improves sensitivity to cortical thinning” ISMRM abstract (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com http://secure-web.cisco.com/" claiming to be https://secure-web.cisco.com/1bhEHVI_wdXl_mLwpwWSqHCKW0qpfVsSGTa6OP2rDyN8h_S...https://secure-web.cisco.com/1me4RY0enlek75e3PAqIseSGOO7tfF84eBwPlWXYndHKO5G2tJADVy-TNvBizJR-LC2_sMvVChG7l5Pa8fM2tIAiP3DQT-SSQTQqRMUoLjOtjqu6MziPDQmMNRY5acq-T2Ufgp-DfTUhXPmCjLOm0i9Su5AxbRJ9lgN0NROMe0D3NZQJ0s72k_2YyzwWh9hncuI8MPyo0OJm0D5IdIvd_8-X2QAvcS54AE_ctHqeQi5RdtlySv2EfrrbKcuNkH5npl63jHoUptIM9QgGYk0XMO4RsHZYRXlfQW1IXJ1n62rfuX8xXiSbcBFppSYPx0utW1SkV7zhUcfnHb0qhtJwUFw/https%3A%2F%2Farchive.ismrm.org%2F2020%2F1050.html https://secure-web.cisco.com/1bhEHVI_wdXl_mLwpwWSqHCKW0qpfVsSGTa6OP2rDyN8h_SQEuJtTL1Bp8YHjzANH8rsJ5sHIKLq7gAJkuuM1H86WIChMxaXgBgvC2iC23AkgfntCssGgMBcVDMPxb9gn52JM9bgfoJaxbhQwk1R2GUVh9k8AoCqP0Uc1dMX-m5ylU3pAHt_8VSh3VKdxbIvAyrumtnw-Gf9v0BLOZa_9jipH4onGhWJgrfzHlsy0zeP37uvHSdD9Fp97Yylqub0ewbCWh-7EmuM0plUYwvrQ17rurRUtYfR3yAY1Pbka7nqV0sAeG7DU_HMt11igojv_/https%3A%2F%2Farchive.ismrm.org%2F2020%2F1050.html%3Chttps://secure-web.cisco.com/1me4RY0enlek75e3PAqIseSGOO7tfF84eBwPlWXYndHKO5G2tJADVy-TNvBizJR-LC2_sMvVChG7l5Pa8fM2tIAiP3DQT-SSQTQqRMUoLjOtjqu6MziPDQmMNRY5acq-T2Ufgp-DfTUhXPmCjLOm0i9Su5AxbRJ9lgN0NROMe0D3NZQJ0s72k_2YyzwWh9hncuI8MPyo0OJm0D5IdIvd_8-X2QAvcS54AE_ctHqeQi5RdtlySv2EfrrbKcuNkH5npl63jHoUptIM9QgGYk0XMO4RsHZYRXlfQW1IXJ1n62rfuX8xXiSbcBFppSYPx0utW1SkV7zhUcfnHb0qhtJwUFw/https%3A%2F%2Farchive.ismrm.org%2F2020%2F1050.html%3E) as well as related code on Github (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com http://secure-web.cisco.com/" claiming to be https://secure-web.cisco.com/1pmfGJ-rEOTUEdebbVReP2FLewbwtarzsq0OiG8ICt0vhxO...https://secure-web.cisco.com/10WRpCPnvc4D9H2TOaZHsTUn0u7cWtVKoReU9EtexFnzvs4ApXqcGX5LXIAqA1gw_jDyZM0n74IRnrQrlh-uC5HiUAB3QqdEQ4zL9c8zhF_OLGSzGLytRBv-qE6DlzxoJtfknjZSMHEk9AVKlDkNKUwBjYFIOBfFv0DA9Yeb5gqDUcqqZAprEL025Pp2xpCpTM3ZS5Qm_zuM2FG1j0boLUTmrLOeHCk3ls6LB6hI03mwTM2feKe8q6B2xiqJvcLmC8dKpj0jL8EEzZNi8PpkbFflk3RYfghezpSY7yOXY-dgVEzNbcZOVNd4lNmn-aZBLK1zqNqtODLsPG0JOP_Q3wA/https%3A%2F%2Fgithub.com%2Fmu40%2Ffreesurfer%2Ftree%2Fnf-long-nonlin https://secure-web.cisco.com/1pmfGJ-rEOTUEdebbVReP2FLewbwtarzsq0OiG8ICt0vhxOCLMW3VEjO6v0Wb2z6BblHPBf1eNZgxV7CyUkIyJIe5nZ8-mtZEmFCD_szDXdl-AoMSP1aa-xt_8aSDhaEIJdv0_68QlV7kezkzDixPag2Qnui0jwTxumyld3WRa1XLDHr6e8F9sPMQqbNfSLpER0x1DrfEGw2AD6cxIF1DK5qHUGxdJRTle6E01gM6Y3xGDHU-X9-G4tBawlict3MMzneyqiXGSdRMIr7nyKvYtCH1mJTGXDMOtYor8JoXIqlFQiIETEF6dFYz3jyOQvLr/https%3A%2F%2Fgithub.com%2Fmu40%2Ffreesurfer%2Ftree%2Fnf-long-nonlin%3Chttps://secure-web.cisco.com/10WRpCPnvc4D9H2TOaZHsTUn0u7cWtVKoReU9EtexFnzvs4ApXqcGX5LXIAqA1gw_jDyZM0n74IRnrQrlh-uC5HiUAB3QqdEQ4zL9c8zhF_OLGSzGLytRBv-qE6DlzxoJtfknjZSMHEk9AVKlDkNKUwBjYFIOBfFv0DA9Yeb5gqDUcqqZAprEL025Pp2xpCpTM3ZS5Qm_zuM2FG1j0boLUTmrLOeHCk3ls6LB6hI03mwTM2feKe8q6B2xiqJvcLmC8dKpj0jL8EEzZNi8PpkbFflk3RYfghezpSY7yOXY-dgVEzNbcZOVNd4lNmn-aZBLK1zqNqtODLsPG0JOP_Q3wA/https%3A%2F%2Fgithub.com%2Fmu40%2Ffreesurfer%2Ftree%2Fnf-long-nonlin%3E).
I was wondering whether you could provide insights into what you think the best strategy for obtaining reliable longitudinal cortical thickness measurements in such a dataset. Do you have a feel for whether the Longitudinal Freesurfer processing stream still provides benefits over Cross-Sectional analysis in the presence of large defects? Would you recommend giving the above-mentioned non-linear implementation a shot or were there other reasons the feature has not been implemented yet in the official version?
Thanks already in advance!
Best
Philip The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1wwv94s7JtpES2h6FAik4D5_2xCE945ev4VBoQNeiMICUNf... https://secure-web.cisco.com/1wwv94s7JtpES2h6FAik4D5_2xCE945ev4VBoQNeiMICUNfHxHVu_Hgt9MMUjiScnMVVGOZRK2UofFIB5uRtcOygbZyPJZ41HTj4xiRoijjVUcZvqhY781I8N-V2zpKN8126yStXG1PZvsqkbw-xtX-Eml0RrWlFhQeZNZvtHwafHMnck4fBpVxg9KuM-QYbDpnb5_Uv61Xqfs-2rK20kSywnH8VWhg3cbXSJatqIDw6yDniH4O2cfhnYcRJJGlpVf77n5cieQJ-MmvkUzbTSCX9AULELvWxFQakNkoaiuNAmmfoOUlA_8Td4cEy-XGxV/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1OZiXAu2zz935CJvxBcUz1zxYk_E0-TCi601mn7OnJLBJ_O... https://secure-web.cisco.com/1OZiXAu2zz935CJvxBcUz1zxYk_E0-TCi601mn7OnJLBJ_OyVuUCrPXXIlhEfomqzVyYSjtYikY4qK7APGlqIbDh_XfbNaInJ0wn8itmTTLEJLbr0Y0s1C2qgAVtTuft-iQUm9zK-irWAIQeZtiS9sm84gKM8L-Kk748Hn1OSZ4xucnMEFr3qp-oclkQPAP3e_pBZmUZIy2mXq3PKIIM7YR8mFG3aRv5xuvIld4nm04pBlc1JksBlwdtfGANqkQ2E1T9AuT2s0N85psb_BDNcpisHYGHFDV4JGvwBOCWLpESkdK3ktyRPn6RThhjUZX6BRHTdomePwPw8gPaa7ElYFQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .
freesurfer@nmr.mgh.harvard.edu
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Hoffmann, Malte,PhD -
Philip P