Hi Marisa,

usually a random time point is selected as an initial registration target. From there we map all images (including the initial target) to a common mid space and create the first template there, then we register to that template and iterate. This speeds things up, but is theoretically not totally unbiased (due to the special role of the initial target). Now since all get resampled, this potential bias is very small (i.e. could not be measured) , so I selected this to be the default in the interest of having a fast registration. Further the randomness across subjects will remove any potential remaining bias in a group analysis.

Now if you specify no init, we will first create a really bad looking template, register to that and iterate (so it is completely unbiased), but will take much longer to converge. I don’t recommend doing this.

Best, Martin

On 17. Sep 2020, at 15:12, Marisa Johanna Nordt mnordt@stanford.edu wrote:

Hi,

I have a question regarding the flag -- inittp 0 (no init ) in mri_robust_template. What does ‘no init’ mean in this context and which consequences arise from using this flag?

Thank you! Best, Marisa

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