Hello Mark,
Thank you for the help, it is appreciated.
All the best,
Jacob
> Dear Jacob,
>
> I'm not quite sure what you want to see in standard space, but
> renderhighres is what I would usually use for a single session. However,
> using applywarp would achieve the same goal. Trying to run a higher-level
> analysis with one input probably isn't such a good option though.
>
> All the best,
> Mark
>
>
> On 11 Apr 2014, at 14:20, [log in to unmask]
> <[log in to unmask]> wrote:
>
>> Hello again FSL experts,
>>
>> I am wondering if someone can provide a bit of insight into which option
>> may make more sense for working with single session data/1 run in
>> standard
>> space?
>>
>> Below are a few options I think may work, but I am not certain which may
>> be best or if there are other complexities that I may be over looking.
>>
>> 1. applywarp to the First-level analysis stat images.
>> 2. Run a Higher-level analysis even though my input is a single
>> session/run. Would this option reapply statistical constraints and/or
>> misrepresent the original stat values?
>> 3. I have used renderhighres before, but this seems to only transform
>> the
>> z-stats and I am not sure which transformation is being applied.
>>
>> I have provided more details in my previous emails below, but please let
>> me know if you have any questions.
>>
>> Thank you for the help.
>>
>> Jacob
>>
>>
>>> Hello Stephen,
>>>
>>> Thank you for your reply and for the information. I think in an attempt
>>> to
>>> provide a few different solutions, my question may have gotten a bit
>>> lost.
>>>
>>> For all runs within the cohort, I have worked from the same .fsf file
>>> and
>>> scripted in the appropriate information. My concern about the
>>> registration
>>> steps, only refers to my attempt at manually applying the registration
>>> transformations to the subjects that have 1 run, and for this project,
>>> had
>>> not yet been run through a FEAT Higher-level analysis.
>>>
>>> For the subjects with 2 runs, these have been combined in a FEAT
>>> Higher-level analysis (Fixed Effects) and I have been able to extract
>>> the
>>> relevant data from their stats in standard space. For the subjects with
>>> only 1 run, I would like to work with their stats in standard space as
>>> well.
>>>
>>> I am wondering, if I only include the 1 set of first level cope images
>>> in
>>> a FEAT Higher-level analysis, will this reapply statistical constraints
>>> and/or misrepresent the original stat values?
>>>
>>> If so, would I be better off applying the registration matrices to the
>>> FEAT First-level stat images that are in native functional space?
>>>
>>> I am hopeful that this email and my question is a bit more clear and
>>> maybe
>>> now some of the possible solutions I mentioned previously will make a
>>> little more sense.
>>>
>>> Thank you again for the help!
>>>
>>> -Jacob
>>>
>>>
>>>
>>> Hi - all runs will have their stats transformed into standard space
>>> using
>>>> the same set of tools, if you setup FEAT registration in the same way
>>>> in
>>> all runs - this is still true even if you have multiple runs per
>>> subject
>>> or one, with the standard way of doing things in FEAT. Even when you
>>> combine several runs together from a single subject (eg using a
>>>> higher-level fixed-effects FEAT), all those runs got transformed into
>>> standard space before that higher-level analysis.
>>>>
>>>> Cheers.
>>>>
>>>>
>>>>
>>>> On 2 Apr 2014, at 03:15, [log in to unmask]
>>>> <[log in to unmask]> wrote:
>>>>
>>>>> Hello FSL Experts,
>>>>> I have three hopefully simple registration questions/possible
>>>>> solutions
>>> that I would appreciate your insight into.
>>>>> I am working on an analysis that requires data from individual
>>> subjects'
>>>>> fMRI stats. For the majority of the cohort, subjects have multiple
>>> runs,
>>>>> which have been combined into higher-level analyses. For those
>>>>> subjects
>>> with only 1 run, and thus only a first-level analysis, I want to be
>>> certain that I am applying the same registration transformations as has
>>> been done in the higher-level analyses (FLIRT and FNIRT).
>>>>> Option 1. Considering the group level analysis I am working on will
>>>>> be
>>> constructed manually, I am wondering if I can simply make copies of the
>>> one run only .feat directories and then combine the same subjects'
>>> identical copes in a higher-level analysis? I am a bit skeptical of
>>> this
>>>>> approach because I am not sure if combining identical copes in a
>>> higher-level analysis may have an effect on the statistics, as in, I am
>>> not sure if the combining of copes and the generated stats factor in
>>> some
>>>>> form of weighting that would ultimately misrepresent the original
>>> stats.
>>>>> Option 2. Assuming that Option 1 not only expose my ignorance to how
>>> cope
>>>>> images are combined, but also introduces a weighting error to the
>>> generated stats, I am wondering if there is a way to modify
>>>>> renderhighres
>>>>> to apply the proper transformations matrices to all the stats?
>>>>> Option 3. Considering I am using both FLIRT and FNIRT, I am wondering
>>> if
>>>>> the example_func2standard.mat is the only transformation I need to
>>> apply
>>>>> and if I can use applywarp directly to the stat images from the
>>> first-level analyses?
>>>>> I have gone to the log files for the multi-run subjects to take a
>>>>> look
>>> at
>>>>> the command lines, and there seems to be a few applywarp commands
>>>>> used.
>>> This leads me to believe that I may need to apply several
>>>>> transformations
>>>>> in order to replicate what has been applied to multi-run subjects
>>> higher-level stats, but again, I am not certain.
>>>>> In summary, if you can please point me in the general direction of a
>>> solution I would be sincerely grateful.
>>>>> Thank you for the all of the help and please let me know if I may be
>>> missing or overlooking any details.
>>>>> Much appreciated,
>>>>> Jacob
>>>>> The information in this e-mail is intended only for the person to
>>>>> whom
>>> it is
>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>> the
>>> e-mail
>>>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>> you
>>> in error
>>>>> but does not contain patient information, please contact the sender
>>>>> and
>>> properly
>>>>> dispose of the e-mail.
>>>>
>>>>
>>>> ---------------------------------------------------------------------------
>>> 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
>>>> ---------------------------------------------------------------------------
>>>>
>>>> Stop the cultural destruction of Tibet
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>
>
>
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