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stoppel | 8 Jun 16:59

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Prestimulus FIR

Hey everybody,

just a short question. Does anybody know if it is possible to extract  
the FIR timecourses not only for the time after an event onset, but  
for the prestimulus period?

Thanks in advance

Chris

Dr. med. Christian Stoppel
Klinik für Neurologie
Universitätsklinikum Magdeburg A.ö.R
Leipziger Str. 44, 39120 Magdeburg
Tel.: +49 - 391 - 6117 537
Fax.:+49 - 391 - 6117 531

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adrzezga | 8 Jun 18:08

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simple VOI-analysis

Hi

I am looking for a way to perform a very simple VOI-analysis on resting
state fMRI-data in Nifti-format using with Marsbar.

I want to

1.) import my own predefined ROI/VOI in Nifti-Format
2.) Apply this VOI on a number of images (N > 1), which have not been
included into a predefined SPM-design matrix before
3.) Read out mean, max and standard deviation within this VOI on every
single scan included (not across all images). That means: Mean value image
1 = x, Mean value image 2 = y, Mean value image 3 = z, etc.

Somehow, I cannot figure out how to do this with Marsbar, as it appears,
that the programs sticks to predefined SPM.mat design files. However I
want to include images outside of a predefined SPM design matrix.

Is there a simple way to do this very basic analysis ?

I appreciate any advice !

Alex Drzezga

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(Continue reading)

Matthew Brett | 8 Jun 21:08

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Re: [SPM] estimate question using marsbar

Hi,

> I have some error when I process estimate in marsbar
>
> (E=estimate(D,Y) or using the button 'estimate result')
>
> Initialising parameters                
:                   ...computing???
> Index exceeds matrix dimensions.

This might be the inversion of the covariance failing, try this FAQ entry:

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

- does that help?

Best,

Matthew

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john brooks | 10 Jun 00:03

spm8

hello,
marsbar does not work with spm8 and seems not to launch. 
is there a way to fix this?
 the errors are:
Warning: This usage of "spm ver" is now deprecated. 
  In spm at 811
  In mars_utils at 222
  In marsbar at 99
  In marsbar at 57
  In spm at 910
Warning: Name is nonexistent or not a directory: 
/Applications/matlabthings/spm8/toolbox/marsbar/spm6. 
   In path at 110
  In addpath at 87
  In marsbar at 108
  In marsbar at 57
  In spm at 910
MarsBaR analysis functions prepended to path
??? Undefined function or method 'mars_veropts' for input 
arguments of type 'char'.
Error in ==> marsbar at 112
mars_veropts('defaults');
Error in ==> marsbar at 57
marsbar('on');
Error in ==> spm at 910
    evalin('base',xTB(i).prog);
??? Error while evaluating uicontrol Callback

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john brooks | 16 Jun 01:07

Re: spm8

I determined an apparent fix for those who are interested.
1.  duplicate the folder /spm8/toobox/marsbar/spm5
2.  rename the folder to /spm8/toolbox/marsbar/spm6

then marsbar should launch within spm8.

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elisa.marchetta | 17 Jun 09:47

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Data extraction without using SPM design

Hi everybody,
I used Marsbar to extract BOLD signals from fMRI images.
I chose the 'full option' extraction and said NO to the Question "Use  
SPM design?".

Moving this way I noticed that the parameter about SPM design remains  
empty, so can I be sure about having extracted the raw data without  
any filtering or similar?

Thanks in advance
Elisa Marchetta

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stoppel | 17 Jun 13:13

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PSTH for time before events

Hey,

does anybody know if it is possible to extract a PSTH not only or the  
period after an event, but also for the time preceding it?

Greetz

Christian

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Matthew Brett | 19 Jun 07:24

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Re: PSTH for time before events

Hi,

> does anybody know if it is possible to extract a PSTH not only or the
> period after an event, but also for the time preceding it?

Sorry, at the moment, you can't do that easily - except by subtracting
some number from your event onsets before making the model.  It would
be a good feature to add though...

Best,

Matthew

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Matthew Brett | 19 Jun 07:25

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Re: Data extraction without using SPM design

Hi,

> I used Marsbar to extract BOLD signals from fMRI images.
> I chose the 'full option' extraction and said NO to the Question "Use
> SPM design?".
>
> Moving this way I noticed that the parameter about SPM design remains
> empty, so can I be sure about having extracted the raw data without
> any filtering or similar?

Yes - but in fact - even if you do use the design, the extraction does
not use the filtering.  It would use the session scaling though,

Best,

Matthew

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Matthew Brett | 19 Jun 07:29

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Re: [SPM] MARsbar % BOLD Question

Hi,

> I'm trying to do ROI % signal extraction in marsbar and everything seems fine
> until I select % signal change then I get the error
>
> need fMRI design for % signal change

The percent signal change routines need some estimate of the
event-related response - for this you need an FMRI design, with
events, basis functions and so-on.  It's possible to imagine percent
signal change for things like PET designs, but it requires some
thought about what is the baseline and so on.

Best,

Matthew

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Recent entries

raw vs. standardized % BOLD signal change (10 Feb 15:20)
Extract ROI data using command line (8 Feb 20:48)
[SPM] Build Marsbar ROIs (7 Feb 20:09)
Import/Build ROI (6 Feb 12:23)
loading an existing .nii file using maroi_image (2 Feb 19:31)
loading an existing .nii file using maroi_image (2 Feb 18:32)
I: ROI (2 Feb 11:29)
ROI (25 Jan 11:48)
Help for extracting values using Marsbar (21 Jan 02:02)
importing binary masks in marsbar (19 Jan 11:23)
ROI (18 Jan 10:17)
import issues - help much appreciated! (16 Jan 18:16)
% signal change (2 Jan 23:45)
error (23 Dec 20:24)
get_marsy error (12 Dec 21:27)
Error in extracting ROI (5 Dec 23:41)
Export summary timecourse, and factorial designs with pre-whitening (1 Dec 05:22)
Averaging over ROI (30 Nov 13:44)
% signal change and baselines (28 Nov 02:43)
0.43 bugfix release - please read - please upgrade (20 Nov 01:59)
Release next week (13 Nov 07:54)

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