Patrick Williams | 24 Jan 07:26
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Help with error message

Hi Marsbar users,

I am trying to use the script:

roi_files = spm_get(Inf,'*roi.mat', 'Select ROI files');
des_path = spm_get(1, 'SPM.mat', 'Select SPM.mat');
rois = maroi('load_cell', roi_files); % make maroi ROI objects
des = mardo(des_path);  % make mardo design object
mY = get_marsy(rois{:}, des, 'mean'); % extract data into marsy data object
y  = summary_data(mY);  % get summary time course(s)

---------------------------------------------------------------------------------------------------

When I do so I select an ROI from the ROI's that go with MarsBar (left amygdala in this case) and then select the SPM.mat for the participant I want to look at. When I do so I get the following error, which I know is common:

??? Error using ==> spm_sample_vol
Cant open image file.

Error in ==> maroi.getdata at 103
  data = spm_sample_vol(data_imgs(i),...

Error in ==> maroi.get_marsy at 76
  [y vals vXYZ mat]  = getdata(o, VY);

Error in ==> NarrAmyg at 5
mY = get_marsy(rois{:}, des, 'mean'); % extract data into marsy data object

---------------------------------------------------------------------------------------------------

I followed the directions in the FAQ and reset the path to the images, but I still get the error.

I am using SPM8 in MatlabR2009. Can anyone suggest a possible fix for my problem?

Best,
Patrick B. Williams

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Matthew Brett | 29 Jan 00:33
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Re: Help with error message

Hi,

> ??? Error using ==> spm_sample_vol
> Cant open image file.

> I followed the directions in the FAQ and reset the path to the images, but I
> still get the error.

Hmm - I don't know.  After you've reset the path to the images, have
you tried reloading the design into marsbar, and rechecking that the
image path?

If that works (ie the fix completed correctly, maybe you could try
turning the matlab debugger on:

>> dbstop if error

running the script, and then using the debugger to go up the stack to
see if you can see which filename is causing the problem?

best,

Matthew

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Matthew Brett | 20 Jan 13:50
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Re: [SPM] A question about % signal change in MarsBaR

Hi,

On Wed, Jan 20, 2010 at 3:04 AM, fenglu <fenglu <at> fingerpass.net.cn> wrote:
> Hi, Matthew. Thank you for help. I think I have got to know how to compute % signal change.
> First, when we compute fitted time course, the time course due to an event is averaged between sessions.
Second, we got the value of top half signal for this time course as 'd'. Then 'd' is divided by mean of the
session and we got a 's'. Last, we average the 's's across a session.
> All the calculations above is voxel-based.

Nearly - the fitted time courses are per-session, and then divided by
their own session means, then, if you've selected to get signal change
across sessions by combining events, these are averaged to get the
final result,

Best,

Matthew

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Matthew Brett | 19 Jan 18:30
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Re: [SPM] A question about % signal change in MarsBaR

Hi,

I've Cc'ed the marsbar mailing list; it's the best place for marsbar questions.

> Event_signal is a function which I thought to be the key to my question. So
> I read the source code.
>
> 0053 for e_i = 1:e_s_l
> 0054   es    = e_spec(:, e_i);
> 0055   ss    = es(1);
> 0056   Yh    = event_fitted(D, es, dur);
> 0057   d     = pr_ev_diff(Yh, diff_func, varargin{:});
> 0058   s     = s + d ./ s_mus(ss,:);
> 0059 end
> 0060 s = s / e_s_l * 100;
>
> Question1. So I think by default 'd' is the absolution of max(fitted event
> time course).

This code gets the fitted time course, and then uses the pr_ev_diff
function to calculate the value for the top half of the signal change
from the event time course.  The default method is 'abs max' which
returns the value that has the absolute maximum, that is, the most
positive value if that is greater than the abs of the most negative
value, otherwise the most negative value.

> But what does 'ss' mean? Is it the number of session according
> to the definition of 'e_spec'? But it is said that s_mus is the mean of
> blocks. So 'ss' is the number of block, am I right? I am confused.

Yes, 'ss' is the the session number - for example if you have two
sessions ss can either be 1 or 2.

> Question2. For ER Design, there is no block. How can I use this method?

Well, there are sessions in a block or event related design.

> Question3. Is 'e_s_l' the number of session?

It's the event spec length - the number of events the routine is working on...

Best,

Matthew

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Richard Binney | 15 Jan 15:01

calculation of statistics

Hi Matthew,
 
I'm just wondering if you can clarify something for me?
 
For simplcitiy sake, let me start with the T-stat.  What does Marsbar divide the mean beta/weighted sum beta by to get the t-stat.  It doesn't appear to be the standard error of the betas.  From looking at the MarsS structure, it seems like it might be extracting info from the ResMS file associated with the SPM.mat file of the design, but what exactly and where can i find these figures/calulcations in the MarsS structure?
 
Similarly, should I use a a full factorial design, what is Marsbar using for the F-test?
 
Many thanks
 
Richard
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Matthew Brett | 15 Jan 15:54
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Re: calculation of statistics

Hi,


> For simplcitiy sake, let me start with the T-stat.  What does Marsbar divide > the mean beta/weighted sum beta by to get the t-stat.  It doesn't appear to > be the standard error of the betas.  From looking at the MarsS structure, it > seems like it might be extracting info from the ResMS file associated with > the SPM.mat file of the design, but what exactly and where can i find these > figures/calulcations in the MarsS structure?
Marsbar gets the residual mean squared error from the ResidualMS matrix in marsbar's saved version of the SPM.mat ('_mres.mat'). It then uses this with the design matrix covariance and the contrast to get the estimated error of the contrast statistic. It should be mathematically identical to SPM. The calculations are - for SPM2 designs and above - in <marsbar>/@mardo_2/private/pr_stat_compute.m. In there, you'll find these lines for the T statistic: con(i,:) = xCon(ic).c'*betas; VcB = xCon(ic).c'*SPM.xX.Bcov*xCon(ic).c; stat(i,:) = con(i,:)./sqrt(Hp*VcB); where xCon(ic).c is the contrast matrix, VcB is the variance of the covariances of the betas, and Hp is the residual mean squared error. Best, Matthew ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev
jizheng zhao | 8 Jan 16:51
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How the ROI should be defined in PSC calculation?

Dear all:

        I have a question about the ROI definition and PSC calculation. When we calculate the PSC of ROIs, whether those ROIs must be identified by an independent data (or sessions). Could we get the ROIs and calculate their PSC in the same data?

  

Best regards.

                                       cliff

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Matthew Brett | 8 Jan 23:10
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Re: How the ROI should be defined in PSC calculation?

Hi,


>         I have a question about the ROI definition and PSC calculation. When > we calculate the PSC of ROIs, whether those ROIs must be identified by an > independent data (or sessions). Could we get the ROIs and calculate their > PSC in the same data?
It's possible to get the % signal change from the ROI, if you found ROI with the same comparison, but of course the value will be biased by the selection, so you could not sensibly use the % signal change value to - for example - compare to other ROI / % signal change estimates. Best, Matthew ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev
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Sien Hu | 15 Dec 20:46
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[marsbar] error message

Dear marsbar users,

I'm deriving the effect size of each ROIs from each subject and have succeeded
in getting stats from 9 out of 11 ROIs. For the other 2 ROIs, marsbar showed me
this error message in matlab's command window.

Error in ==> maroi.getdata at 30
if nargin < 2

??? Output argument "vXYZ" (and maybe others) not assigned during call to
"/Applications/spm8/toolbox/marsbar/ <at> maroi/getdata.m (getdata)".

Error in ==> maroi.get_marsy at 76
  [y vals vXYZ mat]  = getdata(o, VY);

These 2 ROIs were tiny spots so I suspect that these regions might reflect
noise. Is the size of the ROI one of the reasons that result in this error
message? What should I do to fix this problem if I really want to get the stat
from these ROIs?

Many thanks!

Sien

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Matthew Brett | 15 Dec 20:50
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Re: [marsbar] error message

Hi,


> I'm deriving the effect size of each ROIs from each subject and have succeeded > in getting stats from 9 out of 11 ROIs. For the other 2 ROIs, marsbar showed me > this error message in matlab's command window. > > > Error in ==> maroi.getdata at 30 > if nargin < 2 > > ??? Output argument "vXYZ" (and maybe others) not assigned during call to > "/Applications/spm8/toolbox/marsbar/ <at> maroi/getdata.m (getdata)". > > Error in ==> maroi.get_marsy at 76 >  [y vals vXYZ mat]  = getdata(o, VY);
Is it possible you've hit this problem?: http://marsbar.sourceforge.net/faq.html#why-do-i-get-a-no-valid-data-for-roi-warning-when-extracting-data Best, Matthew ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev

Gmane