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Registering Images to a Template - antsMultivariateTemplateConstruction2.sh #1760
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Can you provide a complete collection of commands you have used, and examples of the inputs, outputs and clearly indicate what you thing is insufficient about the results. |
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Sure. I'll just show T1w images, but the template was construced using T1w, T2w, FA and MD.
The other attempts using normalised subject's images didn't help with matching 3) either. To answer you, @gdevenyi , there is a noticeable difference in the cortical areas and that's where my attention will go for the next steps of my processing. The warped images retured by Thanks again, |
The only pre-processing that should happen in the template script is N4BiasFieldCorrection, which is done if the It's hard to gauge from screen caps how different the results are. There will be some run-to-run variability because of random sampling in the affine stage. Also, your output from the template script is registered to the previous template - after each set of pairwise registrations, the template is updated. After the last run, the final template is generated, so the registrations are out of date. However, you can find template (n - 1) under the Sharpening is done on the template, not the individual images, so that's not it. Dividing the images by their mean is done during averaging after registration. |
I think this is where the unexpected difference arises. |
I noticed that, as the images were labelled as "Repaired", but the dataset I'm using is already preprocessed, so I left it out for now. I might include it, just in case.
As @gdevenyi pointed out, sounds like this could be the clarification I was after. I'll just run a quick test using the (n-1) template. That would not be relevant when working with subjects outside the template population, but it will be hopefully a good way to confirm that this is what causes these differences.
I confirm I only sharpened the template's images (T1w, T2w, FA, MD). That step makes sense to me, although it didn't have much effect on the final result, as the template images would generally be smoother that the subjects'. Thanks you both for clarifying. I'll run some more tests and I'll report here the results. |
Dear experts and developers,
I am dealing with a template that was generated with HCP subjects with the
antsMultivariateTemplateConstruction2.sh
script.So, I started using those template images (T1w, T2w, FA, MD) as fixed images and correspondent subject's images as moving images for the
antsRegistrationSyN.sh
script. I felt like the results were sub-optimal and, surprisingly enough, I found out that the subject I was trying to register to the template belongs to the population that was used to construct the template. So, I compared the subject warped to template returned byantsMultivariateTemplateConstruction2.sh
to the subject I registered to the template withantsRegistrationSyN.sh
and they look significantly different.After making sure that the preprocessing of the images used for the template construction and my subject were exactly the same, I made some attempts to hopefully improve the registration result:
antsMultivariateTemplateConstruction2.sh
are normalised by their mean, so I did the same for my subjectantsRegistrationSyN.sh
using a Laplace approachUnfortunately I haven't had success, so far.
Is there anything I am missing? Next step for me would be to match the parameters set of the
antsRegistration
call made withinantsMultivariateTemplateConstruction2.sh
, but I feel like I am maybe missing some other fundamental steps.The aim of all this is to replicate the registration made within
antsMultivariateTemplateConstruction2.sh
and use the same approach to register any subject to a template. Could I get some information on how the template/subject registration is performed withinantsMultivariateTemplateConstruction2.sh
?Thanks,
Simone
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