Marsbar with spm 8

Hi,

I am trying to use the new marsbar version with spm 8. I can open marsbar en
I can view my rois. However, marsbar does not recognise any of the spm.mat
files when I try to set the design from file, even though they are present
(it also does not recognise spm5 mat files).

I use matlab 7.4.  I open marsbar by typing marsbar in the command window,
because it does not show up in the toolbox button. 

Can anyone help?

Cheers,

Maya

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ROI within an ROI

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Re: Marsbar with spm 8

O and I forgot to say that I tried; 
setappdata(0,'UseNativeSystemDialogs',false) as suggested in a message on
the 28th of July. I am using windows.

Hope anyone can help!

Cheers,

Maya 

mayaVisser wrote:
> 
> Hi,
> 
> I am trying to use the new marsbar version with spm 8. I can open marsbar
> en I can view my rois. However, marsbar does not recognise any of the
> spm.mat files when I try to set the design from file, even though they are
> present (it also does not recognise spm5 mat files).
> 
> I use matlab 7.4.  I open marsbar by typing marsbar in the command window,
> because it does not show up in the toolbox button. 
> 
> Can anyone help?
> 
> Cheers,
> 
> Maya
> 
> 

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Re: Marsbar with spm 8

More problems!

I am now using my colleagues' computer. I can now set the design from file.
He is using a 64 processor whereas I am using a 32 processor, does that make
a difference? (i copied his spm8 folder directly onto my computer and I
still could not retrieve the design file)

However, when I try to choose a ROI (extract ROI data) I get the following
error message

Fetching data                           :                         1/1   ???
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 ==> marsbar at 985
marsY = get_marsy(o{:}, VY, sumfunc, 'v');

Error in ==> spm at 957
evalin('base',CBs{v-1})

??? Error while evaluating uicontrol Callback

>>

This looks similar to the problem of Dr. Rachel Mitchell (message on 28 of
July). I tried typing mardo_5, but it does not make a difference. 

Hope anyone can help!!!

Cheers,

Maya

mayaVisser wrote:
> 
> O and I forgot to say that I tried; 
> setappdata(0,'UseNativeSystemDialogs',false) as suggested in a message on
> the 28th of July. I am using windows.
> 
> Hope anyone can help!
> 
> Cheers,
> 
> Maya 
> 
> 
> 
> 
> 
> mayaVisser wrote:
>> 
>> Hi,
>> 
>> I am trying to use the new marsbar version with spm 8. I can open marsbar
>> en I can view my rois. However, marsbar does not recognise any of the
>> spm.mat files when I try to set the design from file, even though they
>> are present (it also does not recognise spm5 mat files).
>> 
>> I use matlab 7.4.  I open marsbar by typing marsbar in the command
>> window, because it does not show up in the toolbox button. 
>> 
>> Can anyone help?
>> 
>> Cheers,
>> 
>> Maya
>> 
>> 
> 
> 

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Re: Marsbar with spm 8

Hi,

> I am trying to use the new marsbar version with spm 8. I can open marsbar en
> I can view my rois. However, marsbar does not recognise any of the spm.mat
> files when I try to set the design from file, even though they are present
> (it also does not recognise spm5 mat files).

I assume from your later message that you mean that the GUI does not
display the SPM.mat files?

Have you tried selecting the SPM.mat files by typing in the name in
the GUI?  Does that work?

Best,

Matthew

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Re: Marsbar with spm 8

Hi,

> However, when I try to choose a ROI (extract ROI data) I get the following
> error message
...
> Fetching data                           :                         1/1   ???
> Error using ==> spm_sample_vol
> Cant open image file.

Did you try the suggestions in the FAQ?

http://marsbar.sourceforge.net/faq.html#why-do-i-get-an-error-cant-open-image-file-when-estimating-a-design

Best,

Matthew

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Re: [SPM] Marsbar in SPM8

Hi,

> I used SPM8 now, but when I tried to load the design from my SPM.at file
> ("set design from file"), no SPM.mat file was read (but SPM5 allows it).

I think you want the marsbar list for this (I've Cc'ed it).

Do you mean that the SPM.mat files don't appear when the 'select
design' GUI comes up?   The matlab GUI appears to vary a bit between
platforms and versions.  What platform are you using (Linux, Windows,
Mac, version).  What Matlab version do you have?

Best,

Matthew

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Re: Marsbar with spm 8

Dear Matthew Brett,

Thank you very much for your replies. It is working now and I am very happy
about that! 

Best wishes,

Maya

Matthew Brett wrote:
> 
> Hi,
> 
>> I am trying to use the new marsbar version with spm 8. I can open marsbar
>> en
>> I can view my rois. However, marsbar does not recognise any of the
>> spm.mat
>> files when I try to set the design from file, even though they are
>> present
>> (it also does not recognise spm5 mat files).
> 
> I assume from your later message that you mean that the GUI does not
> display the SPM.mat files?
> 
> Have you tried selecting the SPM.mat files by typing in the name in
> the GUI?  Does that work?
> 
> Best,
> 
> Matthew
> 
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> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> 30-Day 
> trial. Simplify your report design, integration and deployment - and focus
> on 
> what you do best, core application coding. Discover what's new with 
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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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Comparison questions in MarsBar

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Re: Comparison questions in MarsBar

Hi,

On Mon, Sep 14, 2009 at 4:23 AM, Vladimir Luo <bntac <at> yahoo.com.tw> wrote:
> Dear users, In my experiment, I want to compare the response to a stimulus
> temperature (ST) in a specific brain region between group 1 and 2. The ST
> raised from a baseline temperature (BT). I have the following 2 questions:
> (1). I used MarsBar to obtain the percent signal change (%SC) in this brain
> region. I calculated: S1: %SC for ST in group 1 S2: %SC for ST in group 2
> B1: %SC for BT in group 1 B2: %SC for BT in group 2 Then: %SC for the ST
> raised from the BT in group 1 = S1 – B1 %SC for the ST raised from the BT in
> group 2 = S2 – B2 Did I do it correct? (2). I found that (S2 – B2) is
> significantly larger than (S1 – B1). Then, I want to know if the baseline
> activity in this brain region is the same between the 2 groups, i.e. if B1 =
> B2. Can I directly use the %SC of B1 and B2 obtained by Marsbar to represent
> the baseline activity in this brain region? I appreciate for any help.

Am I right in thinking that you have no baseline other than BT?  That
is, the whole time of the experiment is either BT or ST?  In that case
it will be very noisy estimating the signal change for ST and for BT.
  In particular, the absolute values for BT, and ST, will be very
noisy.  The difference between BT and ST should be OK though.

Best,

Matthew

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