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>
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 <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/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>)
> 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-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>).
>
> 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
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