See in line responses below.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Office: (773) 406-2464
=====================
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On Sun, Jun 26, 2011 at 6:45 AM, Kavita Vemuri <[log in to unmask]> wrote:
> Hi
>    My experiment is to measure response to different types of music and visual stimuli. The subjects are given no task but have to freely listen or view a clip.
>
> For the music test: I have music in which the tempo changes abruptly. But each tempo is played for at least 80 seconds. I tried many designs as given below:
> 1) Tempo1 : Onset 1 50
>            duration 30
>   Tempo2: onset 75 125
>           duration 30
> t-contrasts: 1 -1 (tempo1 - tempo2) and -1 1 (tempo2 - tempo1)
> 2) Tempo1 : Onset 1
>            duration 60
>    tempo1a : onset 10
>              duration 20
>    tempo1b: onset 30
>             duration 20
>  (similarly for tempo 2. This was to take care of any saturation because of the long durations).
>   Contrast (gets very confusing here) : 0 1 -1 (for set of conditions covering tempo1 duration) and 0 1 -1 (for the tempo2)
>  Of course, there are many combinations here, but the idea is to remove any saturation effects while comparing tempo1 response to tempo2.
>
> Question 1: Am i doing something wrong or is the design OK?

Both seem like fine options. The other way to do it is to use a time
modulator. The contrast for the second one is testing if the second
part of the sounds is different from the third. Its not comparing the
two tempos. If you want to compare tempos, then the contrast needs to
be between the 2 tempos (e.g. 1/3 1/3 1/3 -1/3 -1/3 -1/3
>
>
> As suggested by you, I also did ICA (GIFT) and have the temporal & spatial map for each subject.
> Question 2: Can I compare the region of interest as seen in the GLM/SPM to that  obtained from ICA? I see that people have looked at it independently.

You can compare the temporal components to the SPM.xX.X matrix from
the SPM processsing. I forget the the name of the file on the GIFT
side that stores the timecourses.

corr function in MATLAB will do the correlation
regress function in MATLAB will provide the stats for each column

the plot function also works well.

if you want to overlay 2 plots, you can use "hold on" to hold the
current plot and add a second plot.


>
> I really appreciate all help, as confusion has set in as I do more & more analysis.
>
> regards
> Kavita
>
>
>
>
> ----- Donald MCLAREN <[log in to unmask]> wrote:
>> What are you trying to detect?
>>
>> When you set up your design, it creates an expected hemodynamic response. It
>> then tries to fit that to your data.
>>
>> Your blocks need to relate to something in the task and not be random. If
>> you truely have a random pattern that you have no expectation when the brain
>> comes on and turns off, then you should be using ICA.
>>
>> Best Regards, Donald McLaren
>> =================
>> D.G. McLaren, Ph.D.
>> Postdoctoral Research Fellow, GRECC, Bedford VA
>> Research Fellow, Department of Neurology, Massachusetts General Hospital and
>> Harvard Medical School
>> Office: (773) 406-2464
>> =====================
>> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>> intended only for the use of the individual or entity named above. If the
>> reader of the e-mail is not the intended recipient or the employee or agent
>> responsible for delivering it to the intended recipient, you are hereby
>> notified that you are in possession of confidential and privileged
>> information. Any unauthorized use, disclosure, copying or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited and may be unlawful. If you have received this e-mail
>> unintentionally, please immediately notify the sender via telephone at (773)
>> 406-2464 or email.
>>
>>
>> On Wed, May 18, 2011 at 11:00 AM, Kavita Vemuri <[log in to unmask]> wrote:
>>
>> > Hi
>> >   My experiment has no explicit task(well, that is an oxymoron!) - requires
>> > free viewing of moving images. The fMRI collected is collected TR of 2
>> > seconds and the total duration of the experiment is around 8 minutes . At
>> > the 1st level analysis phase, I notice big variations when 'Onset'(block) is
>> > changed from 20 to 22 with a duration of 20, for example. The design is in
>> > seconds. Is this expected? For example: At an onset = 20 & duration = 20, I
>> > see not even one voxel highlighted but when the onset=22 and the duration=
>> > 22 or 25, there is huge response.
>> >
>> > Question: in an task independent/free viewing paradigm, can blocks be
>> > selected in the design?
>> >
>> > Regards
>> > Kavita
>> >
>
>