MarsBaR ROI toolbox mailing list ()

deutseli | 6 Jun 10:07

AAL ROIs

Hi

In trying to extract raw data from some SPECT images on SPM2 using the AAL ROIs I got the error message

Mapping files : ...done
Fetching data : 1/2 ??? Error while evaluating uicontrol Callback.

To check what was going on I set the image I was using as the structural default and tried to view the ROI on it. The ROI didn't appear. What would cause this? Do the dimensions of my image need to be identical to the dimensions of the MNI template (they're not but why should they have to be) or is there something else obvious that I'm missing?

Many thanks

Elisheva

AOL now offers free email to everyone. Find out more about what's free from AOL at AOL.com.

-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users

headers

s.c.a.n. lab | 6 Jun 21:49

Raw timecourse batch script

Dear Marsbar users,

I am trying to extract the raw signal timecourse from multiple ROIs in over 100
subjects. Although I am able to extract raw timecourses from a single subject
and ROI using the GUI, a batch script would be most helpful. I have tried using
the code in the FAQ, but have not been successful. Does anyone have or know of
any extant scripts that I could adapt to serve this purpose?

Thanks!
Noah

/*
Social Cogntive & Affective Neuroscience (scan) Lab
Yale University, Psychology Dept.
http://pantheon.yale.edu/~scl39/
voice: 203-432-6538
email: scan.lab <at> yale.edu
*/

-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

headers

Matthew Brett | 6 Jun 23:07

Re: Raw timecourse batch script

Hi,

> I am trying to extract the raw signal timecourse from multiple ROIs in over 100
> subjects. Although I am able to extract raw timecourses from a single subject
> and ROI using the GUI, a batch script would be most helpful. I have tried using
> the code in the FAQ, but have not been successful. Does anyone have or know of
> any extant scripts that I could adapt to serve this purpose?

What problems did you have with the FAQ script?

Best,

Matthew

-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

headers

Gwladys Rey | 7 Jun 11:27

4 way ANOVA - export data

Dear all,

Sorry in advance, my question is clearly due my lack of theoretical basis.. !

With data from a ER-fMRI, I’m trying to perform an ANOVA 2×2×2×2 ( 3 way-design and 2 groups) by extracting data from a ROI with Marsbar.

With the function “Export” I can obtain many files.. ( I tried to extract data from two separated 3-way ANOVA performed with SPM ; one for each group).

What are the values (beta, c beta, mean values..) that I have to use in my 4-way anova ? Do I extract data from each subject and each condition?

Thanks you !

GR

-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users

headers

Matthew Brett | 7 Jun 11:38

Re: 4 way ANOVA - export data

Hi,

> With data from a ER-fMRI, I'm trying to perform an ANOVA 2×2×2×2 ( 3
> way-design and 2 groups) by extracting data from a ROI with Marsbar.
>
> With the function "Export" I can obtain many files.. ( I tried to extract
> data from two separated 3-way ANOVA performed with SPM ; one for each
> group).
>
> What are the values (beta, c beta, mean values..) that I have to use in my
> 4-way anova ? Do I extract data from each subject and each condition?

Sadly, I'm afraid you need to collect the data from single subjects by
fetching the betas from the first level analyses from the matlab
workspace.  It's not elegant I know.   So, you would do the stats for
each subject, and, after estimation from the GUI (batch scripts
simpler) do something like:

E = mars_arm('get', 'est_design'); % to get the estimated design from
the interface
B = betas(E);

and then get the beta values you want from the B matrix.

Best,

Matthew

-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

headers

s.c.a.n. lab | 7 Jun 16:53

Re: Raw timecourse batch script

Hi Matthew,

The main problem is that the script doesn't prompt me for separate 
sessions like
the gui does. I thought this might be problematic because I'd like to 
be able to
scale the data for each subject (and/or functional run). Is this possible?

Thanks!
Noah

Quoting Matthew Brett <matthew.brett <at> gmail.com>:

> Hi,
>
>> I am trying to extract the raw signal timecourse from multiple ROIs 
>> in over 100
>> subjects. Although I am able to extract raw timecourses from a 
>> single subject
>> and ROI using the GUI, a batch script would be most helpful. I have 
>> tried using
>> the code in the FAQ, but have not been successful. Does anyone have 
>> or know of
>> any extant scripts that I could adapt to serve this purpose?
>
> What problems did you have with the FAQ script?
>
> Best,
>
> Matthew
>

/*
Social Cogntive & Affective Neuroscience (scan) Lab
Yale University, Psychology Dept.
http://pantheon.yale.edu/~scl39/
voice: 203-432-6538
email: scan.lab <at> yale.edu
*/

-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

headers

Matthew Brett | 7 Jun 19:10

Re: Raw timecourse batch script

Hi,

> The main problem is that the script doesn't prompt me for separate
> sessions like
> the gui does. I thought this might be problematic because I'd like to
> be able to
> scale the data for each subject (and/or functional run). Is this possible?

That will happen by default in the scripts as I remember them, because
it gets the image scaling from the SPM models....

Hope that helps,

Matthew

-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

headers

Peter Wright | 11 Jun 17:13

Exporting data with GLM filter

Dear all,

Ive been trying to get the data out of MarsBar that has been through the 
SPM MC regressor model and can plot it using the Data --> plot full 
command but can only seem to get out the raw data with the Data --> 
Export data command for both the mean ROI time course and all pixels 
within ROI time courses.

The corrected data must be in the memory because it is plotting it, but 
I cant see to get at it. Can anyone help?

cheers!

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 DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

headers

Luijten, M. | 13 Jun 10:54

Extract ROI data - ERROR

Dear Marsbar users,

This week I started using Marsbar and I really like the tool!
However, when I try to extract the data from my 9 ROI's with Extract ROI
data (default) I get for only 7 ROI's the means back. 
The Error for the two missing ROI's is:

Warning: No valid data for ROI 2(clusters_based_on_beta_AL_-32_-40_-28)
	>In maroi.get_marsey at 80
	 in marsbar at 957
	 in SPM at 1276
	 Fletching data

The Error for the other missing ROI is totally the same except from the
ROI name. 
I hope someone can help me with this problem.

Thanks!
Maartje Luijten

-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

headers

Mayuresh Korgaonkar | 14 Jun 23:07

batch for fitted event time course

Hi Matthew,

I was interested in a batch extraction of the fitted event time course using marsbar. I believe the batch code on the FAQ page is for the FIR event response. How would I modify this to extract the fitted event time course?

Thanks,

Mayuresh.

-------------------------------------------------------------------------
This SF.net email is sponsored by DB2 Express
Download DB2 Express C - the FREE version of DB2 express and take
control of your XML. No limits. Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/

_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users

Mon	Tue	Wed	Thu	Fri	Sat	Sun

				1	2	3
4	5	6	7	8	9	10
11	12	13	14	15	16	17
18	19	20	21	22	23	24
25	26	27	28	29	30

17	February 2012
8	January 2012
8	December 2011
29	November 2011
28	October 2011
19	September 2011
15	August 2011
11	July 2011
38	June 2011
39	May 2011
27	April 2011
20	March 2011
26	February 2011
33	January 2011
13	December 2010
16	November 2010
9	October 2010
22	September 2010
4	August 2010
14	July 2010
24	June 2010
10	May 2010
30	April 2010
17	March 2010
3	February 2010
8	January 2010
7	December 2009
4	November 2009
13	October 2009
12	September 2009
12	August 2009
27	July 2009
12	June 2009
7	May 2009
19	April 2009
14	March 2009
13	February 2009
21	January 2009
9	December 2008
17	November 2008
12	October 2008
6	September 2008
9	August 2008
9	July 2008
20	June 2008
11	May 2008
13	April 2008
7	March 2008
5	February 2008
3	January 2008
10	December 2007
19	November 2007
15	October 2007
17	September 2007
24	August 2007
29	July 2007
29	June 2007
21	May 2007
30	April 2007
30	March 2007
19	February 2007
13	January 2007
7	December 2006
5	November 2006
14	October 2006
18	September 2006
25	August 2006
24	July 2006
6	June 2006
18	May 2006
11	April 2006
9	March 2006
19	February 2006
31	January 2006
11	December 2005
19	November 2005
12	October 2005
14	September 2005
30	August 2005
11	July 2005
23	June 2005
13	May 2005
16	April 2005
23	March 2005
38	February 2005
17	January 2005
1	January 2003