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/16FeQmMvpVmDkVtAAQejyFWYwOHvGCtYUAmbwy5l10Qs2126...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of AmirHussein Abdolalizadeh amirhussein.a@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