alignment to MNI template

AFNI Message Board
1

Dear afni people,

I’m trying to be sure of my analyses from the beginning :

What is the best template to align everything (anat of subjects and EPI) to MNI space with afni ?

Could I use “MNI_caez_N27” ? (an by the way what is the difference with “MNIa_caez_N27” ?

I would like after that to use the FreeSurfer brain surfaces in MNI space (Based on the anatomical dataset (N27) obtained from MNI) that we can download from your website.

Thanks a lot for your attention.
Sorry if this question has already been asked…
Alain

2

Hi Alain,

It might be better to get a response from Daniel, but
while he is away…

The MNI152_T1_2009c+tlrc might be a good choice, or
possibly the MNI_caez_N27 dataset you mention. The
former is with 152 subjects but using non-linear
registration (so it is not so blurry).

The MNIa version of N27 would not be appropriate, as
it is in the MNI anatomical space (with AC @ 0,0,0).
The MNI FreeSurfer data that we distribute is in MNI
space, not MNIa (verify with 3dinfo -space).

  • rick
3

Hi Rick,
Thanks a lot for this quick answer.

I would then just have a follow up question :

Let’s say I align all my individuals stats with MNI152_T1_2009c+tlrc
Then I’m doing a t-test on that.
Would it be possible to visualize/project the result on the MNI FreeSurfer data that you distribute on your website (because if I understand well it is surface data from MNI_caez_N27 not from MNI152_T1_2009c)?

My answer (but I would like to check :slight_smile: ) would be yes: open afni with MNI_caez_N27 as underlay and suma at the same time and project the result of the t-test on it.
As everything in in MNI space it would be correct EVEN if the t-test has been done on data aligned with MNI152_T1_2009c+tlrc.
Am I right?

Thanks again
Alain

4

Hi Alain,

That is a good question, though I have to think not.

Well, let’s back up. Are you using non-linear registration?
If so, then do not throw away that relative accuracy by
projecting to an inappropriate surface. If the registration
is only affine, then it probably would not make such a big
difference which surface you project on to, though still,
it would make a modest difference.

I am not sure whether the T1_2009c dataset has sufficient
anatomical delineation to run through FreeSurfer, though it
would be easy to try.

  • rick
5

Hi Rick
Thanks for your answer.
Sorry for being late to write.

Actually I don’t know if I’m using non-linear registration…
I’m just using “@auto_tlrc -base MNI_caez_N27+tlrc” (or with MNI152_T1_2009c+tlrc)…

But you’re rigth I can try to run the recon-all of Freesurfer on the MNI152_T1_2009c+tlrc to see if I can have the surfaces…
thus with both template, I would have the correct surfaces.

Anyway for now i started with MNI_caez_N27+tlrc. It’s just to align 1st level analysis results of all subjects in the same space to run after that a group analysis.
It will be rather easy to try that with MNI152_T1_2009c+tlrc to see the result.

Thanks for your help.
Alain