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FSL  December 2007

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Subject:

Re: mirroring ROI

From:

Steve Smith <[log in to unmask]>

Reply-To:

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

Date:

Mon, 10 Dec 2007 14:12:06 +0000

Content-Type:

text/plain

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text/plain (106 lines)

You should be able to use makerot to create an affine transform to  
achieve what you want (maybe in conjunction with fslswapdim) when  
applied using flirt.
Cheers.


On 10 Dec 2007, at 14:05, Finn Lennartsson wrote:

> Hi,
>
> Yes, the fslswapdim sounds like a good fix to the MST problem given  
> that I have my A/P-axis aligned in y (as in registration to a  
> standard space).
>
> However, some of the data I have will have gross pathology in them,  
> so a registration to standard space is not really realistic.
>
> Therefore I would like to define a "mid-sagital line" myself in  
> relation to anatomy. Any ideas on how this could be done in FSL  
> (without importing into Matlab - where a mirror y of x in a plane  
> with a (normalized) normal n would be y=x-2(x*n)n )
>
> Thanks,
>
> Finn
>
>
>
>
> On Dec 10, 2007 2:46 PM, Saad Jbabdi <[log in to unmask]> wrote:
> Hi Finn.
>
> Just to add to what Matt suggested. If you want a MST mirroring,  
> then you will have to have your ROI in standard space first.
>
> Cheers,
> Saad.
>
> On 10 Dec 2007, at 13:39, Matt Glasser wrote:
>
>> Finn,
>>
>> A simple way to do that might be to create a copy of the ROI and  
>> then run fslswapdim –x y z on it.  This should give a "mirrored" ROI.
>>
>> Peace,
>>
>> Matt.
>>
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask] ]  
>> On Behalf Of Finn Lennartsson
>> Sent: Monday, December 10, 2007 5:23 AM
>> To: [log in to unmask]
>> Subject: [FSL] mirroring ROI
>>
>> Hi,
>>
>> I have a ROI that I would like to mirror in a plane (e.g. the mid- 
>> sagital plane), so that a corresponding "mirror ROI" is created on  
>> the other side of the plane.
>> Not sure if I can use straight forward linear algebra with fslmaths  
>> (with a voxel-based projection formulae), or whether a flirt  
>> transform (rotation or translation) might do it?
>>
>> So the input in my case would be a ROI-image and a (user-defined)  
>> in-plane line/vector.
>>
>> Has anyone done this? Any advice would be appreciated!
>>
>> Thanks in advance,
>>
>> Finn
>
> ---------------------------------------------------------------------------
> Saad Jbabdi,
> Postdoctoral Research Assistant,
> Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 222545   (fax 222717)
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~saad
> ---------------------------------------------------------------------------
>
>
>
>
>
>
>
> -- 
> _______________________________
> Finn Lennartsson
> Rödabergsbrinken 8
> SE-113 30 Stockholm, Sweden
> Cel. + 46 704 838907
> E-mail: [log in to unmask]


---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------

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