PSC from trials with different durations

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Re: PSC from trials with different durations

Hi,

> I have trials with different durations (e.g. 3, 6, 9, 12 seconds).
> My question: is it valid to compare percent signal change values of these
> different durations with each other?
> Or is it possible that higher percent signal change values in conditions
> with longer durations result from the longer trial duration?
> Thank you for  your help!

It will be difficult to compare the signal from these events.  The
longer events will generate more prolonged activation and therefore
higher signal change given the same neural activation per unit time.
Even if you adjust for the event length you are relying on the signal
change per unit time being proportional to the neural activity per
unit time, requiring strict linearity of the hemodynamic response per
unit time of the neural response, which is unlikely...

Best,

Matthew

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Re: signal change

Hi,

Sorry to be slow to reply, I have been in the US for a while and am
slowly catching up on work email.

> - should i use the betas or the con-files to get an impression about the
> time course of activation in my roi?

No - the beta images and therefore the con images (which are just
combinations of beta images) summarize over the whole time course, and
therefore have no time information in them.

You will have to go back to the original single subject designs and
data to get time course information.

> - if i choose the beta-images, can i calculate my own % signal change by
> subtracting the value of the baseline consition from the values of each of
> the 4 conditions in session2 ?

To get percent signal change, the easiest option would just be to use
the marsbar interface on the single subject data, rather than going
through the route of getting information out of the beta images and
replicating the marsbar calculations in matlab.

Best,

Matthew

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Re: signal change

dear matthew brett.

thanks for your reply about my question according the signal changes.
this topic seems to be very complicated (at least for me). so may i ask
2 follow up questions?

if i use the raw signals from my images (example with 3 sessions, each
designed with 20 scans), what options should i use in marsbar?

is it ROI extraxtion (full data) and then the single images of each
session 
- with help of the spm.design (which contains information about the
sessions and the scaling) 
- or should i choose without help of the spmdesign (what 'scale gran
mean' should i choose?).
The differences between these options are marginal, but with help of the
spm design it is much more comfortable.

final question:

if i got (for my example) 60 scores out of marsbar, i am interested of
the ROI-intensities in my 3 sessions and in my two groups of subjects. 
to control for individual differences (due to different baseline
intensities (first session)) i would calculate the percent of signal
change of the 2nd and 3rd session in relation to the first session.
is this correct? 

if so, can i answer my question about differences of activity between my
two groups by a simple t-test of the percent signal changes of session 2
in relation to session1?

i know, this simple questions must be ignoring for you. but after
working with spm and marsbar a while, i don't trust my statistics
knowledge anymore (if i ever had one).

so your help is much appreciated.

thanks a lot

yours markus

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Undefined command/function 'spm_get'

Dear all,

when i try to extract FIRs from a ROI with Marsbar i receive the 
following error message (under both linux or win xp).
Undefined command/function 'spm_get'

spm_get.m indeed does not exists in SPM5. going to SPM2, where it exists 
i receive further errors...

could anyone prevent me from going nuts totally?

thanks a lot

Gyula Kovacs

-- 
Gyula Kovacs

Dept.Cognitive Sciences
Budapest Univ. Technology and Economics
Hungary H-1111 Stoczek u 3 III.318
T:0036-1463-1176
F:00361463-1072
---------------

Dept. Psychology
Inst. Psychology
Univ. Regensburg, Germany
T:0049-941-943-3852; 
Mobile:0049178 1725506
Fax:0049 941 943 3233 

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Re: Undefined command/function 'spm_get'

Gyula Kovacs wrote:
> Dear all,
>
> when i try to extract FIRs from a ROI with Marsbar i receive the 
> following error message (under both linux or win xp).
> Undefined command/function 'spm_get'
>
> spm_get.m indeed does not exists in SPM5. going to SPM2, where it exists 
> i receive further errors...
>
> could anyone prevent me from going nuts totally?
>
> thanks a lot
>
> Gyula Kovacs
>
>
>
>
>   
It seems you do not have all marsbar path.
if you type "marsbar" first, it should initialize all needed path (and 
spm_get is defined in marsbar )

hope it's help

Romain

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voxel coordinates in a maroi_pointlist?

Dear Matthew,

I'm using some marsbar functions inside my own custom-written analysis 
code. I'd like to have access to the voxel coordinates (in matlab matrix 
units) of a marsbar-roi that's under the form of a maroi_pointlist... My 
code looks like this for now:

  R  = maroi(fname);
  R_space = native_space(R);
  [pts vals] = voxpts(R,R_space);

First, I'm not really sure what I'm doing with the native_space 
function. Can you confirm this is correct?

Second: how can I convert the values I thus get in the 'pts' variable 
into matlab matrix coordinates? (I mean, coordinates I could use to 
extract the data from a 3D matrix after having read it with something 
like data = spm_read_vols(spm_vol(data_fname)) )

Hoping to make (at least some) sense here, thanks in advance for your help!

Sylvain

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Re: Undefined command/function 'spm_get'

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Re: signal change

Hi,

> if i use the raw signals from my images (example with 3 sessions, each
> designed with 20 scans), what options should i use in marsbar?
>
> is it ROI extraxtion (full data) and then the single images of each
> session
> - with help of the spm.design (which contains information about the
> sessions and the scaling)
> - or should i choose without help of the spmdesign (what 'scale gran
> mean' should i choose?).
> The differences between these options are marginal, but with help of the
> spm design it is much more comfortable.

It depends what kind of analysis you want to do next.  Usually you do
want the automatic corrections to the session means that SPM provides.
 Occasionally you do not, or you do not have an SPM design containing
the images, and the raw options are good for this case.

You might want to have a look at:

http://imaging.mrc-cbu.cam.ac.uk/imaging/PrinciplesStatistics

for some details on how the options for mean scaling work.

> if i got (for my example) 60 scores out of marsbar, i am interested of
> the ROI-intensities in my 3 sessions and in my two groups of subjects.
> to control for individual differences (due to different baseline
> intensities (first session)) i would calculate the percent of signal
> change of the 2nd and 3rd session in relation to the first session.
> is this correct?

Er - not sure.  Do you mean each of the 20 scans in sessions 1-3 refer
to a different condition, and that you have sets of 3 sessions for two
different groups of subjects?
Could you say more about what the scans are, and the experimental design?

Best,

Matthew

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Re: Question about extracting raw BOLD signals

Hi,

> I am a graduate student in Yale University, and now doing some analysis
> using SPM. Currently, I need to extract raw BOLD signals from the GLM model.
> I found spm_regions which does it. But spm_regions ask a structure
> containing specific SPM, distribution & filtering details. So I use
> spm_results_ui to get such required structure, xSPM. However, spm_results_ui
> contain some GUI features asking about the p-values.
>
> My question is: Is it necessary to specify p-values? If not, how can I do to
> avoid it? If I am mistakenly using spm_results_ui, which function should I
> use to get xSPM?

Sorry to say, I have never used SPM regions. You could of course use
marsbar to do a similar thing - but if you want to use spm_regions you
probably ought to try the SPM list - unless anyone else on this list
can help you...

Best,

Matthew

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