Sterling Johnson's lab here at UW-Madison is working on creating a group 
averaged macaque atlas for volume registration. However, we aren't quite ready 
to make them public as there are a few bugs still being worked out. We have 
been using SPM to coregister T2W and T1W images. I'd assume FSL-FLIRT would 
have similar results. 

The best approach might be as follows:
1) Register T2W to T1W
2) Register T1W to F99 (downloadable from SUMS); if you need .img format there 
are many tools available to convert HEAD/BRIK to hdr/img. I believe you can 
load them in CARET and save them as an img file, although I might be wrong.
3) Multiple the 2 transforms to get the T2W to F99 brain; Apply the transform 
using FSL.

Hope this helps.

Best Regards, Donald McLaren
=====================
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Tel: (773) 406 2464
=====================
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----- Original Message -----
From: Hamied Haroon <[EMAIL PROTECTED]>
Date: Monday, March 12, 2007 10:31 am
Subject: [caret-users] Registering Individual Macaque to F99 template
To: caret-users@brainvis.wustl.edu


> Hello,
> 
>  
> 
> I'm a completely fresh novice learning how to use Caret 5.5.
> 
>  
> 
> I was wondering if anyone could give me some advice on the following,
> please...
> 
>  
> 
> I have a single whole-brain T2-weighted structural MRI dataset acquired
> in a post-mortem macaque brain. My dataset is in Analyze format.
> 
>  
> 
> How can I register/deform my individual macaque dataset to the F99
> dataset so that I can then parcellate the temporal lobe according to the
> probabilistic atlases available in CARET_TUTORIAL_SEPT06\MACAQUE?
> 
>  
> 
> If I should use FLIRT in FSL to do the registration then
> 
> how can I get the F99 dataset in Analyze-format to do the registration,
> and
> 
> what options are suggested to be chosen in FLIRT to get the best
> registration results?
> 
>  
> 
> I look forward to receiving your kind advice.
> 
>  
> 
> Thanking you in anticipation.
> 
>  
> 
> Hamied
> 
>  
> 
> ________________________________________________
> 
>  
> 
>  Hamied Ahmad Haroon   PhD  AMInstP
> 
>  Research Associate in MR Neuroimaging
> 
>  Division of Imaging Science and Biomedical Engineering
> 
>  Faculty of Medical and Human Sciences
> 
>  The University of Manchester
> 
>  Room G.603 Stopford Building, Oxford Road,
> 
>  Manchester   M13 9PT
> 
>  England, United Kingdom
> 
>  Tel: +44 (0)161 275 6871   Fax: +44 (0)161 275 5145
> 
> ________________________________________________
> 
>  
> 
>  
> 
>  
> 
> _______________________________________________
> caret-users mailing list
> caret-users@brainvis.wustl.edu
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