Hi,
You want the -paddingsize option in flirt with a value of 1 or 2 - that should be enough.
All the best,
Mark
On 16 Aug 2012, at 16:00, "Rajagopalan, Venkateswaran" <[log in to unmask]> wrote:
> Thanks Steve,
>
> I looked at Flirt page and options -paddingsize comes unde applyxfm so I tried to do the padding using applyxfm but I don't know how to decide on the value that I should enter in the "Extra padding for output FOV" i used 1, 5 etc to see what it is doing it is covering the image portions which were already lost but I am unable to get a complete image yet.
> I looked in the forum archives and FLIRT documention but unable to find answer. So how to choose the value for padding.
>
> Thanks
> Venkat
>
> ________________________________
>
> From: FSL - FMRIB's Software Library on behalf of Stephen Smith
> Sent: Thu 8/16/2012 10:33 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Error when using Flirt
>
>
> Hi - you need more padding slices - see flirt options....
>
>
> On 16 Aug 2012, at 15:18, Rajagopalan, Venkateswaran wrote:
>
>
> Hi All,
>
> I am trying to register my b0 images from two time points unfortunately some of the slices are lost as shown in the PDF attachment.
>
> What parameter do I need adjust anything to do with interpolation I am using now the default settings of FLIRT 12 dof, COST FUNCTION CORRELATION RATIO, interp trilinear interp
>
> Thanks
> Venkat
>
>
>
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> <registration_fail.pdf>
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>
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> Associate Director, Oxford University FMRIB Centre
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> Please consider the environment before printing this e-mail
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> Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010).
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> Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy.
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