MarsBaR ROI toolbox mailing list ()

Re: SPM model and marsbar FIR

Hi,

> I'm new to this forum and I was wondering if the marsbar FIR time-course
> estimation is based on a non-shape assumption even if the original
> SPM-design was modeled with a canonical gamma HRF? So in other words, is the
> time-course analysis dependent on the modelled HRF or is it a different
> disentangeled analysis?

The FIR analysis is inherited from SPM, and what SPM (therefore
Marsbar) does, is to take the original design (with HRF modeling),
extract the event your are interested in, replace the HRF model for
that event with an FIR (non-shape) model, and reestimate.  So, the
event of interest has an FIR model, and all the other events have
their original HRF model.  It's a bit unsatisfactory, because bad fits
in the other events can have odd effects on the event-of-interest FIR,
and it might be better to use a full FIR model for all the events
(although this can soak up lots of degrees of freedom).

Best,

Matthew

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Mario Aparicio | 4 Aug 12:16

can't read SPM.mat files

Hi,

I try to set a design from file but Marsbar 0.41 does not recognize the SPM.mat file (SPM 5; Matlab 7.4). It seems from the Archive list that some users had the same problem. Has anyone found a solution for this?

Thank you very much

Mario Aparicio
Université Libre de Bruxelles (ULB)

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Mario Aparicio | 7 Aug 11:38

Re: can't read SPM.mat files

Hi,

I did not know but a solution to this was posted by Mathew Brett like a year ago: you have to delete “&isunix” in the mars_ufile.m (line 57).

Also, you may have to launch marsbar directly from your matlab window.

Thank you to Kidlab for this information

Mario

ULB

De : marsbar-users-bounces <at> lists.sourceforge.net [mailto:marsbar-users-bounces <at> lists.sourceforge.net] De la part de Mario Aparicio
Envoyé : lundi 4 août 2008 12:16
À : marsbar-users <at> lists.sourceforge.net
Objet : [Marsbar-users] can't read SPM.mat files

Hi,

I try to set a design from file but Marsbar 0.41 does not recognize the SPM.mat file (SPM 5; Matlab 7.4). It seems from the Archive list that some users had the same problem. Has anyone found a solution for this?

Thank you very much

Mario Aparicio
Université Libre de Bruxelles (ULB)

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Jung JeYoung | 7 Aug 13:26

(no subject)

Hello

I'm very new to start using marsbar. I installed it in SPM5 toolbox.
But when I opened it on spm, the window of marsbar didn't appear.
On Matlab, I got the message ;

SPM present working directory:
C:\Program Files\MATLAB\R2006a\work
    ~ - SPM5: marsbar-devel-0.41 toolbox ------------------------------
        Toolbox directory prepended to Matlab path:
        C:\Program Files\MATLAB\R2006a\spm5\toolbox\marsbar-devel-0.41
        ----------------------------------------- 12:01:30 - 07/08/2008

But I didn't get the window.

How can I open it?

Thank you.

Jeyoung Jung

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Matthew Brett | 11 Aug 20:14

Re: (no subject)

Hi,

Did you start marsbar with:

>> marsbar

at the matlab prompt?

Best,

Matthew

On Thu, Aug 7, 2008 at 4:26 AM, Jung JeYoung
<lpzjj <at> exmail.nottingham.ac.uk> wrote:
> Hello
>
> I'm very new to start using marsbar. I installed it in SPM5 toolbox.
> But when I opened it on spm, the window of marsbar didn't appear.
> On Matlab, I got the message ;
>
> SPM present working directory:
>  C:\Program Files\MATLAB\R2006a\work
>     ~ - SPM5: marsbar-devel-0.41 toolbox  ------------------------------
>         Toolbox directory prepended to Matlab path:
>         C:\Program Files\MATLAB\R2006a\spm5\toolbox\marsbar-devel-0.41
>         -----------------------------------------  12:01:30 - 07/08/2008
>
> But I didn't get the window.
> How can I open it?
>
> Thank you.
>
> Jeyoung Jung
>
> This message has been checked for viruses but the contents of an attachment
> may still contain software viruses, which could damage your computer system:
> you are advised to perform your own checks. Email communications with the
> University of Nottingham may be monitored as permitted by UK legislation.
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> _______________________________________________
> Marsbar-users mailing list
> Marsbar-users <at> lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/marsbar-users
>
>

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Manish Dalwani | 25 Aug 19:16

Questions about gray volume through clusters

Dear Marsbar users and Mathew,

I recently learned how to extract mean voxel value (summary time courses) using extract ROI full options on a spm cluster and by exporting it to the matlab workspace.

I have few basic questions. The VBM design I used was in SPM5 using full factorial having 2 groups and 3 covariates. I also used ancova for global normalization. Extract ROI has 2 options 1) obtain raw data 2) From SPM design.

I obtained the raw data first which I assume has not been adjusted for the covariates. When I tried comparing the volumes for the 2 groups using ancova and adjusting for the covariates using SPSS there were no significant differences? Any comment s or suggestions? Maybe I am doing something wrong in SPSS.

If I use the SPM design to get the GM values will it control/adjust for the various design parameters applied including the covariates? Or will it just adjust for global normalization but not for covariates? If I use this option do I have to look for the 'y' or do I still export the summary time course in my matlab workspace to look at the volumes?

Lastly, are the volumes reported in mL?

Kindly advise,
Manish Dalwani
Sr. PRA
University of Colorado

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Matthew Brett | 27 Aug 03:33

Re: Questions about gray volume through clusters

Hi,

>  I obtained the raw data first which I assume has not been adjusted for the
> covariates. When I tried comparing the volumes for the 2 groups using ancova
> and adjusting for the covariates using SPSS there were no significant
> differences? Any comments or suggestions? Maybe I am doing something wrong
> in SPSS.

It's true that marsbar makes no attempt to adjust for the factors in
the SPM model, it only replicated the SPM image scaling for session
effects.  You will need to make sure you have replicated the full SPM
design, including any constant columns, to get something similar in
SPSS.

> If I use the SPM design to get the GM values will it control/adjust for the
> various design parameters applied including the covariates? Or will it just
> adjust for global normalization but not for covariates? If I use this option
> do I have to look for the 'y' or do I still export the summary time course
> in my matlab workspace to look at the volumes?

I would export the summary time course for safety.

> Lastly, are the volumes reported in mL?

The scaling is from the SPM design and the images.  I'm afraid I don't
know what units in VBM scans are, I guess unmodulated would be
probability, and modulated a more complex function of probability...

Best,

Matthew

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