Hi - you could just use fslroi to reduce a 4D timeseries to a subset.
Cheers.
On 3 Jun 2008, at 15:35, Jose Paulo Santos wrote:
> 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
>> --------------------------------------------------------------------------
> -
>> =
>> =
>> =
>> =====================================================================
>
>
---------------------------------------------------------------------------
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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