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FSL  August 2010

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Subject:

Re: Brain distortions with FNIRT

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 31 Aug 2010 09:18:32 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (32 lines)

Hi,

Are you providing FNIRT with the non-brain-extracted
versions of the image and a good affine initialisation?
If so, and you cannot see any other problems with what
you are doing then feel free to upload the dataset to:
   http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and make sure you send us the reference number.

All the best,
	Mark



On 30 Aug 2010, at 18:00, Elizabeth Losin wrote:

> Hello all,
>
> I am  using FNIRT to perform nonlinear registration on a sample of  
> 19 participants.  My registration process uses an intermediate in- 
> plane high-resolution scan to aid in registration of the EPI images  
> to the standard.  The MPRAGE nonlinearly registered into standard  
> space for one participant  is distorted at the top of the brain.   
> The brain looks caved in on one side.  These distortions are not  
> present when linear registration (12 parameter affine) is used  
> instead.  Currently, I am using the FNIRT defaults suggested in the  
> FNIRT documentation for a functional study.  Are there any  
> strategies for fixing this distortion within FNIRT?  Any suggestions  
> would be greatly appreciated.  Thanks.
>
> Liz
>

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