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://www.jeiglesias.com

 

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