Hi Steve,
Thanks so much. I apologize for the questions with evident answers. I was
actually being thrown by the fact that the time courses produced by the Full
Model oscillate steadily every volume, whereas I am accustomed to seeing my
4 rest blocks interleaved with 3 active blocks, as is the result from the
pre-subtraction (and is also the result I used to get when doing the
subtraction in Matlab).
Hopefully my last questions on this issue:
1) I should indeed be using EV3 (zstat5) as my perfusion activation maps &
time courses (just need re-thresholding).
2) If I have a 3ms TE, why is there such a strong "BOLD" component?
3) I normally use the time course of the mean z-score to compute % signal
change, SNR and CNR (just in Excel), but I really cannot see how these
metrics fit in with the Full Model, since the timecourses no longer manifest
my blocks. For example, I compute the percent signal change as the
difference between the average of the active blocks and the average of the
rest blocks, all divided by the average of the rest blocks.
Your help is really appreciated.
Nicole
On Tue, 9 Jun 2009 08:54:30 +0100, Steve Smith <[log in to unmask]> wrote:
>Hi,
>
>Actually - your results look fine - and it's a nice example of the
>full model approach working slightly better than the pre-subtraction
>(which in theory it should be in an ideal world).
>
>Judging from the tsplot outputs, the peak Z is actually higher with
>full model, and there are slightly more supra-threshold voxels (I'm
>comparing zstat1 from each approach). Maybe you're just being thrown
>by the fact that (because the peak Z is lower with pre-subtraction)
>"yellow" corresponds to lower zstats with pre-subtraction - so you see
>more yellow....
>
>Cheers, Steve.
>
>
>
>On 8 Jun 2009, at 13:49, Nicole Pelot wrote:
>
>> Thanks Steve. I have used the Model Wizard; I apologize for the simple
>> question. But even now, when I run it again using the Wizard (rather
>> than
>> perfusion subtraction), it does not seem to give me reasonable
>> output. With
>> perfusion subtraction, I clearly get a very good fit; not the case
>> when
>> using the full model. I have a TE of 3ms, and therefore should have
>> negligible a BOLD component, but this does not seem to be the result
>> of the
>> full model. I then have to wonder whether:
>>
>> 1) I'm somehow misusing the Full Model, even with the wizard.
>> 2) I'm mis-interpreting the output.
>> 3) There's a more fundamental issue with my data.
>>
>> I've uploaded images (152682) to illustrate the issue... Is this
>> what a
>> problem with structured noise would look like (i.e. reason to stick to
>> perfusion subtraction)?
>>
>> Thanks so much,
>>
>> Nikki
>>
>> On Sun, 7 Jun 2009 07:58:36 +0100, Steve Smith
>> <[log in to unmask]> wrote:
>>
>>> HI - have you tried using the model Wizard, as suggested in the
>>> manual? This will do the basic setup for you.
>>> Steve.
>>>
>>>
>>> On 5 Jun 2009, at 19:03, Nicole Pelot wrote:
>>>
>>>> Hi,
>>>>
>>>> I have read the FEAT Perfusion documentation quite a few times now,
>>>> but I
>>>> still cannot figure out how to properly set up my EVs. I have a
>>>> block design
>>>> task: 56s/block, 7 blocks, alternating between rest and active
>>>> (start &
>>>> finish with rest).
>>>>
>>>> My main issue is with EV1. It clearly states that we should be
>>>> modeling
>>>> *rest* times, but that leads me to think of a block design with 0's
>>>> for
>>>> active and 1's for rest. However, the sample design seems to show
>>>> all 1's
>>>> for EV1. Also, what convolution should be applied? None?
>>>>
>>>> I've structured EV2 as I always do to correspond to my block design.
>>>> (On:
>>>> 56s; Off: 56s; Convolution: Double gamma).
>>>>
>>>> EV3, I chose "Interaction", and I made the mean of EV1 zero (but the
>>>> min of
>>>> EV2).
>>>>
>>>> Thank you,
>>>>
>>>> Nicole
>>>>
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> 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
>---------------------------------------------------------------------------
|
