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 <mhoffm...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Philip P > <philip.pruck...@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://secure-web.cisco.com/17N_xqg9IuaXhy0eeSRmExNHOVIHuG1VhD7ehDfM9lhAHQx1DjHxZBZOkIMpkZZmaQvKpod_U13FTUEv4Mjlf_zxtBMz1pQDVTSG1Ftye1JN4xO5M5SG4U9BUMa6MFgUFqBl5WtH2iRGieDTWRqoo8pvi4rCDtBE39N59hFeqN8U5vIB60L2hdNZJDtYXE52DhMQ0DXrzAslz3D1MWe2BGQ_pFz6OGMDL62b5vwC629XpD8V8-BX-ErWqw9btxdnEjeXaz1ok0rmjvz_gpZ-RZtp6dXP-PN-niavD-_2ptdlhNpMhri8khgegNPA8q9FJBtKH9dC14pJoywm04FJvMQ/https%3A%2F%2Farchive.ismrm.org%2F2020%2F1050.html<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/1kHilcnCgkwQrldX6iuJ88RE0UoXG5EVoDzuvrFNtUvMJmI9NVVlU6hLHzV_16j7zCxcIDLMuv0QWeoIUrIxm-VtU7KHbMv7W5aY14QjqJxZnIy61sXLVxGMS9GwOY_P3gKjaPcVtShNSu944zWe8iRW5SqV6JQSeH0YxD8k4cElitgB30TuChwpCxpOZ7LUEvF-eEIsdaBtKcwxqt_LJ6MMWVcWrgi26xNlZvTsutJN2trCkbxFFUlWcw3nXbb6HggJx8gWErRDsEpYDA3cNU1OVgY2z1JTDsjOdzUPetcyO-CxasSZ0zIuz5mcBWsGny_ziEMeOR AnZeds3EIeBhQ/https%3A%2F%2Fgithub.com%2Fmu40%2Ffreesurfer%2Ftree%2Fnf-long-nonlin<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/1rl2yFKAdl2Y2_4nr-RVTrY1c4EFuD0xPFxP3boCfk5ckrz4Wqon96BXir1VgKFXAkhJ9SQfeUf-ltuBeE6NhEzFCnsPIRKYZeRLaXsk58nLN1VMZ9mKUQQ5vKPKyo5Rn5UogTC60qloAHgbgTriDHQoCGMcyT2RMSSMy8heYVUy13leFd-42cVwJsKtZVWJN-OUl-J1QdbGwNd0KkOiAT1MxqBiWAAOGBvMeSn2MQ5SV8BC6Cu9BkCDwlYn-6VItrVXIljiwRsbQ83X6s0hZkOb82gtn1vgx_9w1LEM_bOwXwO8dqI5Ze6ztZQShcrmZY3CY8K99haq22-tIO6sRtA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > > <https://secure-web.cisco.com/1rl2yFKAdl2Y2_4nr-RVTrY1c4EFuD0xPFxP3boCfk5ckrz4Wqon96BXir1VgKFXAkhJ9SQfeUf-ltuBeE6NhEzFCnsPIRKYZeRLaXsk58nLN1VMZ9mKUQQ5vKPKyo5Rn5UogTC60qloAHgbgTriDHQoCGMcyT2RMSSMy8heYVUy13leFd-42cVwJsKtZVWJN-OUl-J1QdbGwNd0KkOiAT1MxqBiWAAOGBvMeSn2MQ5SV8BC6Cu9BkCDwlYn-6VItrVXIljiwRsbQ83X6s0hZkOb82gtn1vgx_9w1LEM_bOwXwO8dqI5Ze6ztZQShcrmZY3CY8K99haq22-tIO6sRtA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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