Dear Serin,

You can use any image you like in place of the standard image.
So in your case I would use S1 for all the runs as the "standard image".
That would generally suffice.  If you found that there was an advantage in having the within-session structural as an intermediate (which would normally only be the case if you had significantly different head positions or their was true anatomical change between the runs) then you could add S2 as the "Main structural image" for the second run (etc.).  However, I would normally expect that direct registration of the functionals to a single, representative structural of that individual would be sufficient.

All the best,
	Mark


On 17 Aug 2012, at 20:01, Serin Atiani <[log in to unmask]> wrote:

> Dear Mark, 
> 
> Thanks for your response.
> 
> I registered the second functional run to the first anatomical as you suggested and that added a reg- directory in the already existing .feat for that run. 
> 
> Now when I try to the do the higher level analysis FEAT to combine the runs. I get an error  that some of the directories haven't been registered. 
> 
> I understand your point about the benefit of going to standard, for our paradigm we might never need to combine the data that way, because we are looking at tuning properties of single voxels in Auditory Cortex AC. We are not interested in comparing areas of activation across subjects but voxel tuning across subjects. And therefore the transformation into standard space introduces an additional layer of processing that might smear or alter what we are trying to measure. 
> 
> So my follow up question: Is it possible to run higher level FEAT without having selected the standard structural option in the registration tab? does the specified image there has to be in standard space,; i.e can I repeat my first level analysis with F1--registered to--> S1(main structural) and also with S1 as standard image, and then F2-->S2 with S1 as the standard image, and then combine the runs using higher level analysis?
> 
> Thanks
> Serin
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Mark Jenkinson [[log in to unmask]]
> Sent: Friday, August 17, 2012 2:32 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Registration, combined analysis in native space
> 
> Dear Serin,
> 
> Just use the first structural image throughout (or the second structural image - it is arbitrary, but you need to only use one and not a mixture).
> In general though, I would recommend going to standard space (with the structural image as the intermediate, "main structural" image) whenever you are doing an analysis.  You can always look at the results in the space of the individual structural images by transforming the outputs, but it will help the analysis to be running all higher-level analyses in the same space (i.e. standard space).
> 
> All the best,
>        Mark
> 
> 
> On 16 Aug 2012, at 17:42, Serin Atiani <[log in to unmask]> wrote:
> 
>> 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
>>>> 
>>>> 
>>>> 
>>>>    ===================================
>>>> 
>>>> 
>>>>    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/>  <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. Thank you.
>>>> 
>>>> 
>>>>    <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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>>>> 
>>>> 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.
>>>> 
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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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>>>> 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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>> 
>