I think Christian's point here was that there is no guarantee that using only 6 out of 7 estimated DOFs will in fact provide a better alignment than 6 DOFs from the start. But you may try. In any case, if you are just after a landmark based alignment to AC-PC a landmark based registration will be more efficient...
Cheers-
Andreas
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Thomas, Adam (NIH/NIMH)
Gesendet: Sonntag, 27. November 2005 03:02
An: [log in to unmask]
Betreff: Re: [FSL] AC-PC alignment
I assumed a 6 DOF registration to the MNI brain would result in poor alignments for brains that were substantially larger or smaller than average. Are there any references where people have tried it?
Cheers,
-Adam
---
Adam Thomas [log in to unmask]
Functional MRI Facility, NIMH/NIH/DHHS
10 Center Dr, Room B1D708A
Bethesda MD. 20892-1148
Phone:301-402-6351 Fax: 301-402-1370
-----Original Message-----
From: Christian Beckmann [mailto:[log in to unmask]]
Sent: Saturday, November 26, 2005 5:42 PM
To: [log in to unmask]
Subject: Re: [FSL] AC-PC alignment
Hi
you can specifically ask for a 6DOF (translations/rotations only) transformation when using the FLIRT GUI or the command line cheers christian
On 26 Nov 2005, at 17:49, Thomas, Adam (NIH/NIMH) wrote:
> The AFNI package has a utility to manually perform "AC-PC"
> alignments on
> structural brain images. This moves brains into a common alignment
> without scaling or warping them which can be desirable for certain
> kinds group analysis using cortical surfaces:
> (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
> cmd=Retrieve&db=pubmed&do
> pt=Abstract&list_uids=16035046&query_hl=1)
>
> I'm looking for an automated way of doing this, hopefully using FLIRT.
> I was thinking of trying to do a 7 DOF alignment between each
> subject's brain and the MNI brain but then only applying the
> translation and rotation portions of transformation. But I'm not sure
> how to go about separating the rotation and translation operations in
> the *.mat file from the scaling.
>
> Can anyone advise how I might accomplish this?
>
> Thanks,
> -Adam Thomas
>
>
> ---
> Adam Thomas [log in to unmask]
> Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A
> Bethesda MD. 20892-1148
> Phone:301-402-6351 Fax: 301-402-1370
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