External Email - Use Caution Thanks Malte, that is very helpful !
> On 01.03.2024, at 08:20, Hoffmann, Malte,PhD <mhoffm...@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.pruck...@gmail.com <mailto:philip.pruck...@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 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 <http://secure-web.cisco.com/>" claiming >> to be >> https://secure-web.cisco.com/1bhEHVI_wdXl_mLwpwWSqHCKW0qpfVsSGTa6OP2rDyN8h_SQEuJtTL1Bp8YHjzANH8rsJ5sHIKLq7gAJkuuM1H86WIChMxaXgBgvC2iC23AkgfntCssGgMBcVDMPxb9gn52JM9bgfoJaxbhQwk1R2GUVh9k8AoCqP0Uc1dMX-m5ylU3pAHt_8VSh3VKdxbIvAyrumtnw-Gf9v0BLOZa_9jipH4onGhWJgrfzHlsy0zeP37uvHSdD9Fp97Yylqub0ewbCWh-7EmuM0plUYwvrQ17rurRUtYfR3yAY1Pbka7nqV0sAeG7DU_HMt11igojv_/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> >> >> <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-rEOTUEdebbVReP2FLewbwtarzsq0OiG8ICt0vhxOCLMW3VEjO6v0Wb2z6BblHPBf1eNZgxV7CyUkIyJIe5nZ8-mtZEmFCD_szDXdl-AoMSP1aa-xt_8aSDhaEIJdv0_68QlV7kezkzDixPag2Qnui0jwTxumyld3WRa1XLDHr6e8F9sPMQqbNfSLpER0x1DrfEGw2AD6cxIF1DK5qHUGxdJRTle6E01gM6Y3xGDHU-X9-G4tBawlict3MMzneyqiXGSdRMIr7nyKvYtCH1mJTGXDMOtYor8JoXIqlFQiIETEF6dFYz3jyOQvLr/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> >> >> <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_2xCE945ev4VBoQNeiMICUNfHxHVu_Hgt9MMUjiScnMVVGOZRK2UofFIB5uRtcOygbZyPJZ41HTj4xiRoijjVUcZvqhY781I8N-V2zpKN8126yStXG1PZvsqkbw-xtX-Eml0RrWlFhQeZNZvtHwafHMnck4fBpVxg9KuM-QYbDpnb5_Uv61Xqfs-2rK20kSywnH8VWhg3cbXSJatqIDw6yDniH4O2cfhnYcRJJGlpVf77n5cieQJ-MmvkUzbTSCX9AULELvWxFQakNkoaiuNAmmfoOUlA_8Td4cEy-XGxV/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> >> <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. 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