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FSL  June 2008

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Subject:

Re: Session optimal length (or duration) in event-related paradigms

From:

Jose Paulo Santos <[log in to unmask]>

Reply-To:

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

Date:

Tue, 3 Jun 2008 15:35:10 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (214 lines)

Hello,

Thanks for the advice.

I use fslsplit to explode de original time series file into n files, each 
one corresponding to one volume. Then I use fslmerge to reconstruct time 
series files with different lengths (or durations), which then I input to 
FEAT to analyze.

Yes, I pay attention to the nonlinearities. In fact, if there is some time 
tolerance, I already realized that is better to increase ISIs (instead of 
more events), to compel events separation.

Kind regards,
Jose Paulo Santos


On Tue, 3 Jun 2008 08:31:28 +0100, Steve Smith <[log in to unmask]> 
wrote:

>Hi,
>
>yes, unless FEAT complains about rank deficiency I would ignore the  
>eigenvalues and just use the "effect required" efficiency calculations.
>
>It is fine to reduce the number of timepoints in your data using  
>fslsplit (I'm not sure why you'd want to use fslmerge) to simulate a  
>shorted experiment and see what effect that makes on the efficiency  
>calculations.
>
>Note though, as described in the paper, the efficiency calculations  
>don't know anything about the nonlinearities that occur as the events  
>get closer and closer together, so be careful there.
>
>Cheers.
>
>
>On 2 Jun 2008, at 15:44, Jose Paulo Santos wrote:
>
>> Hello,
>>
>> Sorry for the confusion. I use the term “efficacy” in the sense that  
>> I use
>> these values to determine if a paradigm is efficacious or not, i.e.,  
>> if
>> they look OK and then I can pursuit with the paradigm, or not, and  
>> changes
>> to the paradigm are required.
>>
>> It’s acceptable to use fslsplit and fslmerge to reduce the number of
>> volumes in the data file to compare the resulting values of Effect
>> Required and “Efficacy”? Or these comparisons aren’t possible?
>>
>> Kind regards,
>> Jose Paulo Santos
>>
>>
>> On Mon, 2 Jun 2008 07:27:16 +0100, Steve Smith <[log in to unmask]>
>> wrote:
>>
>>> Hi - I'm still a little confused as we never call this "efficacy" -
>>> this is a plot of the eigenvalues from a singular value decomposition
>>> of the design matrix - it's not as directly useful or interpretable  
>>> as
>>> the "Effect required" efficiency calculations - if they look ok then
>>> that's good enough.
>>>
>>> Cheers.
>>>
>>>
>>> On 1 Jun 2008, at 23:29, Jose Paulo Santos wrote:
>>>
>>>> Hello,
>>>>
>>>> Yes, I got these values from FEAT (please see attachment; this
>>>> example is
>>>> for 250 volumes). The Efficacy is the right most value in the
>>>> diagonal (I
>>>> didn’t consider the others) and the Mean Effect Required is the mean
>>>> of
>>>> Ci’s.
>>>>
>>>> Kind regards,
>>>> Jose Paulo Santos
>>>>
>>>>
>>>> On Fri, 30 May 2008 08:19:03 +0100, Steve Smith <[log in to unmask] 
>>>> >
>>>> wrote:
>>>>
>>>>> Hi - I'm not sure where these Efficacy numbers come from - not from
>>>>> the FEAT efficiency calculations I think? I'm not sure what these
>>>>> are.......
>>>>> Cheers.
>>>>>
>>>>>
>>>>>
>>>>> On 28 May 2008, at 19:10, Jose Paulo Santos wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I'm trying to establish some kind of method to achieve to the
>>>>>> optimal
>>>>>> length in event-related paradigms.
>>>>>>
>>>>>> I designed a paradigm were I collected 500 volumes. The  
>>>>>> participant
>>>>>> reported at the end that he was exhausted. So I know that 500
>>>>>> volumes were
>>>>>> too much in the human perspective. By the end of the session, the
>>>>>> probability of the participant still being concentrated in the  
>>>>>> task
>>>>>> was
>>>>>> quite low.
>>>>>>
>>>>>> With fslsplit and fslmerge commands, I reconstructed several  
>>>>>> files,
>>>>>> until
>>>>>> 250 volumes, and I analyzed each of them with Feat. The numerical
>>>>>> data was:
>>>>>>
>>>>>> Volumes	Efficacy	Mean Effect Required
>>>>>> 250	0.253		0.938
>>>>>> 312	0.241		0.847
>>>>>> 375	0.251		0.752
>>>>>> 438	0.245		0.740
>>>>>> 500	0.243		0.722
>>>>>>
>>>>>> The rule of thumb for the Efficacy determines that it must be more
>>>>>> than
>>>>>> 0.200, and it was for all volumes. The rule of thumb for the  
>>>>>> Effect
>>>>>> Required determines that it must be less than 0.800. This
>>>>>> requirement is
>>>>>> true only for 375 volumes or more. When this data is plotted, it
>>>>>> seems
>>>>>> that there aren’t significant increases in the Effect Required for
>>>>>> more
>>>>>> than 375 volumes. This is in line when the maps are analyzed: the
>>>>>> 375
>>>>>> volumes map has activations more intense (just a bit) and more
>>>>>> extended
>>>>>> (just a bit) than the 438 and 500 maps. So, 375 volumes would be  
>>>>>> the
>>>>>> optimal length (and duration) of the session. If there is some
>>>>>> clearance,
>>>>>> it would be better to increase the inter stimulus interval (null
>>>>>> event)
>>>>>> than to show more stimuli.
>>>>>>
>>>>>> Is this acceptable? Why the Efficacy didn’t change so much?
>>>>>> Increasing
>>>>>> ISIs would increase the Efficacy?
>>>>>>
>>>>>> Thanks in advance,
>>>>>> Jose Paulo Santos
>>>>>>
>>>>>
>>>>>
>>>>> ---------------------------------------------------------------------
--
>> ---
>>>> -
>>>>> 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
>>>>> ---------------------------------------------------------------------
--
>> ---
>>>> -
>>>>> =
>>>>> =
>>>>> =
>>>>> = 
>>>>> = 
>>>>> ===================================================================
>>>> <design_cov.png>
>>>
>>>
>>> -----------------------------------------------------------------------
---
>> -
>>> 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
>>> -----------------------------------------------------------------------
---
>> -
>>> = 
>>> = 
>>> = 
>>> =====================================================================
>>
>>
>
>
>--------------------------------------------------------------------------
-
>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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