MarsBaR ROI toolbox mailing list ()

exclusive activation

Dear users,

Trying to analyze my data so as to look at activation exclusive of activation in area Y determined in a separate (functional localizer) experiment. Is there anyway of doing this sort of thing in Marsbar?

I’ve tried creating an roi in marsbar using SPM get clusters on the localizer data, exporting, using imcalc to create an exclusive mask i1*-1 and then converting this back into a .mat file in marsbar but it doesn’t seem to like it.

I’d be grateful if anyone could point me in the right direction on this problem.

Regards, Jaclyn

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Billington Jaclyn | 6 Dec 14:01

exclusive activation II

Dear users,

In addition to the previous mail I have managed to create an mask which should show activation exclusive of my localizer experiment blob. However, marsbar won’t process this as an roi. I’m getting the following error:

In ma ...done

??? Out of memory. Type HELP MEMORY for your options.

Error in ==> pr_sum_func at 32

ssy = sum(y.^2, 2);

Error in ==> marsy.summary_data at 59

[Y(:,i) Yvar(:,i)] = pr_sum_func(Ys{i}, s_f, Ws{i});

Error in ==> marsy.resummarize at 8

[t1 t2 o] = summary_data(o, s_f);

Error in ==> marsy.marsy at 330

o = resummarize(o);

Error in ==> maroi.get_marsy at 119

marsY = marsy(r_data, r_info, s_info);

Error in ==> marsbar at 975

marsY = get_marsy(o{:}, VY, sumfunc, 'v');

Error in ==> spm at 1604

evalin('base',CBs{v-1})

Is this because the roi is effectively covering most of the brain? I’d be grateful for any pointers.

Thank you.

Jac

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

Dr Jaclyn Billington

Department of Psychology

Royal Holloway, University of London

Egham, Surrey, TW20 0EX

Tel: +44 (0)1784 414368

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I.Kokal | 10 Dec 16:18

out of memory

Dear users,
I have the following error message in matlab when I try to extract 
fMRI data both with a batch and by using the ROI menu (>Data>Extract 
ROi data(default)). I saw the same complain from other users but the 
treat didnt help me as well as the pack comment.

the error is as follows:

Fetching data: error using zeros
out of memory

error in: ...\Marsbar\@maroi\getdata.m
          Y=zeros(nimgs,dlen);
...

I am using a PC and SPM2 and Matlab version 6.

thank you in advance
idil

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Matthew Brett | 11 Dec 15:35

Re: out of memory

Hi,

On Dec 10, 2007 3:18 PM, I.Kokal <I.Kokal <at> med.umcg.nl> wrote:
> Dear users,
> I have the following error message in matlab when I try to extract
> fMRI data both with a batch and by using the ROI menu (>Data>Extract
> ROi data(default)). I saw the same complain from other users but the
> treat didnt help me as well as the pack comment.
>
> the error is as follows:
>
> Fetching data: error using zeros
> out of memory

I imagine this is because your ROI is very large or you have a very
large number of scans.  Could you try collecting for a subset of scans
or for a smaller ROI?

Matthew

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miao | 11 Dec 17:46

how to do % signal change analysis on the most active voxels in certain ROIs


Hi all, 
I would like to know how to do % signal change analysis on the most active
voxels in certain ROIs (1) if we say 5% top active voxels,  (2) if we say a
fix number like 2000 voxels.
Thank you very much in advance, 
Qing 
--

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View this message in context: http://www.nabble.com/how-to-do---signal-change-analysis-on-the-most-active-voxels-in-certain-ROIs-tp14277799p14277799.html
Sent from the MarsBaR mailing list archive at Nabble.com.

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Michiko Sakaki | 12 Dec 06:44

FIR timecourse for a single event

Dear all,

I am a bigginer of fMRI analysis and I have a question about FIR timecourse.
In my experiment, I have different types of events spaced 2-6 seconds apart 
within a single trial.   I am trying to get an event time course by using FIR model.  
Here is a question: Can I separate a timecourse for the one event from the 
other event?  When I extract a timecourse of a specific event, does this timecourse
reflect brain activation for the other event?
I want to extract a timecourse brain activation that is influenced by a focal event.

Regards,

Michiko

----------------------------------------------
Michiko Sakaki, Ph.D.
Research Fellow of the Japan Society for the Promotion of Science
National Institute of Advanced Industrial Science and Technology
Mailto: m-sakaki <at> aist.go.jp

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Matthew Brett | 12 Dec 19:19

Re: how to do % signal change analysis on the most active voxels in certain ROIs

Hi,

On Dec 11, 2007 4:46 PM, miao <qing <at> isc.cnrs.fr> wrote:
>
> Hi all,
> I would like to know how to do % signal change analysis on the most active
> voxels in certain ROIs (1) if we say 5% top active voxels,  (2) if we say a
> fix number like 2000 voxels.

That's a bit hard because marsbar is designed to work with average
timecourses.  You could try voxel selection techniques like the one in
the FAQ for counting voxels about threshold...

http://marsbar.sourceforge.net/faq.html#percent_activated

Best,

Matthew

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Olivier Dufor | 17 Dec 16:26

ROI and design

Dear all

my experimental design is fairly complex and i have just began using MarsBar.

When I select a cluster from a spm.mat (One sample t-test) the analysis within the ROI is ok

but when I selected a cluster resulting from a complex design ((task A - taskB) - (taskC - taskD)),

I was not able to pass the "set data from file" in the Data menu.

How can i do to examine activations effect in a such contrast analysis (paired-t-test analysis with con00x files) ?

excuse me for my english

Thank you

Olivier

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Mayuresh Korgaonkar | 18 Dec 23:06

error during estimation

Hi Matthew,

I was wondering if you know why I would be getting this error. I get the error while using the 'Results->estimate results' option from the GUI. The error is seen only for a particular subject while using an anatomical ROI mask from an atlas.

###########################################################################

ERROR:

MarsBaR analysis functions prepended to path
Loaded MarsBaR defaults from base defaults
Design reporting                        :                        ...done
Fetching data                           :                        ...done
Summarizing data with summary function: mean
Fetching data                           :                        ...done
Summarizing data with summary function: eigen1
Re-estimating covariance
Re-estimating whitening filter
Initialising parameters                 :                        ...done
Covariance estimate                     :                   ...voxelwise
Model                                   :                      estimation
Temporal non-sphericity (over voxels)   :                  ...estimation
ReML Block                  - 1
ReML Iteration              : 1                            ...7.825566e+008
ReML Iteration              : 2                  & nbsp;         ...4.988903e-003
ReML Iteration              : 3                            ...8.773039e+009
ReML Iteration              : 4                            ...2.408947e-003
ReML Iteration              : 5                    & nbsp;       ...1.370541e+001
ReML Iteration              : 6                            ...1.728841e-003
ReML Iteration              : 7                            ...1.987273e-003
ReML Iteration              : 8                    & nbsp;       ...2.448318e-005
ReML Iteration              : 9                            ...8.401005e-005
ReML Iteration              : 10                            ...2.505988e-005
ReML Iteration              : 11                   &nbsp ;        ...1.535447e-005
ReML Iteration              : 12                            ...8.655333e-006
ReML Iteration              : 13                            ...4.488263e-006
ReML Iteration              : 14                   &nbs p;        ...2.388892e-006
ReML Iteration              : 15                            ...1.733487e-006
ReML Block                  - 2
ReML Iteration              : 1                            ...4.622182e+008
ReML Iteration            &nb sp; : 2                            ...8.448107e-003
ReML Iteration              : 3                            ...1.134000e+012
ReML Iteration              : 4                            ...1.187372e-005
ReML Iteration              : 5                    & nbsp;       ...1.547987e-003
ReML Iteration              : 6                            ...4.146589e+017
Initialising parameters                 :                   ...computing??? Index exceeds matrix dimensions.

Error in ==> spdiags at 114
a((len(k)+1):len(k+1),:) = [i i+d(k) B(i+(m>=n)*d(k),k)];

Error in ==> <at> mardo_2\private\pr_estimate at 128
s = spdiags(1./sqrt(diag(s)),0,nScan,nScan);

Error in ==> <at> mardo_2\private\pr_estimate at 345
SPM = pr_estimate(SPM,marsY);

Error in ==> mardo_2.estimate at 72
SPM = pr_estimate(SPM, marsY);

Error in ==> marsbar at 1264
marsRes = estimate(marsD, marsY, struct(...

Error in ==> spm at 1276
evalin('base',CBs{v-1})

??? Error while evaluating uicontrol Callback.

############################################################################################

--
~Mayuresh

"It is not the strongest of the species that survive, nor the most intelligent, but the ones most responsive to change" -- Charles Darwin.

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Luke | 28 Dec 19:07

Set design error - help

I am running SPM5 in Matlab 7.4.0 (R2007a) on a Windows XP machine.

When running Marsbar 0.41, I cannot select the SPM.mat file created in SPM5 in
order to run a % signal change analysis. The SPM.mat file which physically
exists in the folder, does not appear in the get GUI when I attempt to select
the SPM.mat file to use for the analysis.

Any ideas?

Thanks.

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