Hi
I am new to ANTS and I am getting ver ymuch confused by the procedure of making priors for my sample.
In general, I would like to perform cortical thickness analysis with ANTS on two different datasets.
As far as I see, I can
A) either use the available templates and priors from (https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436).
B) Another option is to create templates and priors from my own sample. Howvere, I am very much confused as how to do it.
1 -I was able to successfully generate my sample-specific template by twice running the
"buildtemplateparallel.sh" once with affine normalization only, to generate the initial_template (as
recommended in the help).
2 - Then I performed the Brain extration on this template.
3 - To cretae the probability of the brain-extraction mask the output of step 2 should be smoothed?
i.e. SmoothImage 3 outputBrainextraction.nii.gz 1 outputBrainextractionprob.nii.gz 1
Q1: In this case for example if I choose to use the templates and
priors of IXI sample (that matches best the age-range of my
participants), I could use the IXI-template without any further warp
to my data. right?
Yes.
3 - To cretae the probability of the brain-extraction mask the output of step 2 should be smoothed? i.e. SmoothImage 3 outputBrainextraction.nii.gz 1 outputBrainextractionprob.nii.gz 1
Yes.
Now to generate the priors form my sample, I need to do what?
The suggestion in "antsCookTemplatePriorsExample" seems really circular.
In the first step it runs "antsCorticalThickness.sh" and there it already inputs 4 priors.
How shall I create these 4 priors for my sample?
I can see how that can cause confusion. So even if one wants to create their own template with priors, you need to have access to an existing template and priors, like the templates from figshare. So when it says to run antsCorticalThickness on your template, you need to use that existing template and priors.
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Hi
I am new to ANTS and I am getting ver ymuch confused by the procedure of making priors for my sample.
In general, I would like to perform cortical thickness analysis with ANTS on two different datasets.
As far as I see, I can
A) either use the available templates and priors from (https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436).
B) Another option is to create templates and priors from my own sample. Howvere, I am very much confused as how to do it.
1 -I was able to successfully generate my sample-specific template by twice running the
"buildtemplateparallel.sh" once with affine normalization only, to generate the initial_template (as
recommended in the help).
2 - Then I performed the Brain extration on this template.
3 - To cretae the probability of the brain-extraction mask the output of step 2 should be smoothed?
i.e. SmoothImage 3 outputBrainextraction.nii.gz 1 outputBrainextractionprob.nii.gz 1
Bests
Shahrzad
Last edit: Shahrzad Kharabian Masouleh 2020-01-10
Yes.
Yes.
I can see how that can cause confusion. So even if one wants to create their own template with priors, you need to have access to an existing template and priors, like the templates from figshare. So when it says to run
antsCorticalThicknesson your template, you need to use that existing template and priors.Thanks a lot. It makes now more sense. So now one more question regarding the "antsCookTemplatePriors" example:
Bests
Shahrzad
You can download them from here. Look in "training-labels/*6Labels.nii.gz".
Thanks a lot. Using these, I have now created succesfully the template and priors for my cohort.
Bests
Shahrzad