Dear all,
In my experiment subjects were taken out in the middle of an fMRI session and for that we have two structural scans for each fMRI session. I need my higher level FEAT analysis that combines the functional runs from that fMRI session to be in native space and not in standard space. To do that I believe I need to register the second structural image to the first structural image . I did that using flirt.
My question is the following: when I fill in the registration tab in FEAT GUI for the functional runs that were collected after the second structural image, which structural image should I put in the 'Main Structural' text box, the second structural image or the registered second structural image(registered to the first structural)? and is that enough to make sure that the higher level analysis that combines the runs is all relative to the first structural image?
Thanks
Serin
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
Sent: Thursday, August 16, 2012 11:54 AM
To: [log in to unmask]
Subject: Re: [FSL] Error when using Flirt
Hi,
You could try a larger value, but this is really just extending the original volume beyond its valid FOV, so it is hard to know whether this would be actually useful in your application. The blank areas represent parts where there is no information provided from the original image, so you should think about whether further padding is useful.
All the best,
Mark
On 16 Aug 2012, at 16:48, "Rajagopalan, Venkateswaran" <[log in to unmask]> wrote:
> Hi Mark,
>
> Thanks, I tried both 1 and 2, 2 gave better results than 1 but still I have image portions missing.
>
> Thanks
> Venkat
>
> ________________________________
>
> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
> Sent: Thu 8/16/2012 11:40 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Error when using Flirt
>
>
>
> 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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>>
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>>
>> <registration_fail.pdf>
>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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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>>
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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).
>> Visit us online at http://www.clevelandclinic.org <http://www.clevelandclinic.org/> for a complete listing of our services, staff and locations.
>>
>>
>> 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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>> Thank you.
>>
>
>
>
> ===================================
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010).
> Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations.
>
>
> 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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> Thank you.
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