External Email - Use Caution Dear Amir,
We don’t have a script to make templates, but I don’t think it’d be too hard to do it yourself. You can start from eg MNI (not a problem to start from an existing atlas since your first iterations will be linear anyway), and use the usual procedure: Initialize A = MNI For linear_iterations = 1, …, 5 1. Linearly register every case to current estimate of A 2. Average all registered cases to compute new estimate of A For nonlinear_iterations = 1, …, 5 1. Nonlinearly register every case to current estimate of A 2. Average all registered cases to compute new estimate of A Does this make sense? Even on the CPU, this shouldn’t take more than a few hours, depending on how many cases you have. Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/16FeQmMvpVmDkVtAAQejyFWYwOHvGCtYUAmbwy5l10Qs2126acP7d71U_W6BHTGst-P7LeKA62K-pr-FMfK9GjOE7IZG2h626hZ1CTqDCcckKE4ljY1TIyUBIk6JGppXJyOeducVa5qWiRszT9L9NiXXURWyfG1Tc9Y7ecwtHH7BDmviAanX9YRKOcNwSF2U-7Umaf6O-9HgsUvX-m5mHFngTzRYFQia4ziBA9tTcy5CTa8AQ9t2RKTGYoay3x7b_/http%3A%2F%2Fwww.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AmirHussein Abdolalizadeh <amirhussei...@gmail.com> Date: Wednesday, April 26, 2023 at 09:30 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] EasyReg for group-average template? External Email - Use Caution Dear Freesurfer users/experts, I am working on a research project that requires generating group-average templates from a large sample of data. I wonder about the possibility of using mri_easyreg for generating group-average templates. To my knowledge, the best current pipeline is based on using ANTs that 1) do not support GPU, 2) take ages to generate a template esp. from a large sample of data. I wanted to know, do you have any suggestions to use mri_easyreg for such purposes? I would greatly appreciate any suggestions or advice you can provide. Best, Amir
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