Be careful with hand editing templates built by Dartel. Dartel alignment is driven by the gradients of the logarithms of the values in the templates. Hand editing has probably changed some of the values to zero, which could potentially mess things up. The use of logs comes from the assumption that the template encodes the mean of a categorical distribution (https://en.wikipedia.org/wiki/Categorical_distribution). A template GM voxel of exactly zero is basically saying that there should never ever ever be any trace of GM in that location, so the algorithm will totally freak out and break if a GM voxel does occur there.

Best regards,

-John

On Fri, 11 Jan 2019 at 19:01, Stewart, Peter <[log in to unmask]> wrote:

Hi Everybody,

I have a question and I would very much appreciate input from DARTEL experts. The short version is: I have a hand edited TPM (it was created by registering a set of 202 individuals using DARTEL and then hand editing the final template to enhance accuracy and eliminate extraneous voxels). I would like to warp some new scans into the TPM space. Given that the final template is hand edited, I’m unsure how to proceed (i.e., using the set of templates 1-6 would not correspond exactly to the final TPM, because they are not hand edited). One idea I had was using the templates created en route to the hand edited TPM as the first templates, and then selecting the TPMs as the final template for the registration. This would hopefully have the increased robustness benefits of using a full set of templates while getting everything into the right space with the final step. The other idea was to create templates 1-5 (or actually 2-4, if I recall you only need 5 for Run Dartel: Add to Existing Template) via smoothing the TPMs by kernels of varying sizes to make progressively more blurred images (essentially the reverse of what DARTEL seeks to do, by making increasingly crisp templates). I’m happy to provide more context if it would be helpful.

Any ideas on which approach might be better, if there is any difference, and if it’s the second approach, what factors might I want to smooth by? I greatly appreciate your comments, so thank you in advance.

Peter

Peter V. Stewart, Psy.D. | Staff Neuropsychologist | Assistant Program Director, Neuropsychology Postdoctoral Training | Neuropsychology Internship Coordinator | Geisinger Health System | [log in to unmask]

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