structural MTratio ROIs

Hi 

I have a question regarding ROIs we have defined within the anatomical
structure of the Substantia Nigra for every subject on its MT image (using
MRICRO). As we have more than 40 subjects and 4 different ROIs for each
subject I am looking for a script I can apply in SPM5 which can extract the
mean values of each structural ROI we have defined. 

Can I use MarsBaR for structural ROIs too? If yes, how can I change the .roi
(output format from MRicro) format into a format I can use in MarsBaR?
Mricro only has the option to change a ROI into an analyse format.

Thanks for your help =)

Sandra
--

-- 
View this message in context: http://www.nabble.com/structural-MTratio-ROIs-tp21836875p21836875.html
Sent from the MarsBaR mailing list archive at Nabble.com.

------------------------------------------------------------------------------
Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM)
software. With Adobe AIR, Ajax developers can use existing skills and code to
build responsive, highly engaging applications that combine the power of local
resources and data with the reach of the web. Download the Adobe AIR SDK and
Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com

[SPAM] Newsletter for February

Dear sir/madam,

I know you're probably sceptical about the various claims made for
Feng-Shui, but just think about this for one moment: If Feng-Shui were not
accurate or useful, would it have survived more than 3,000 of years?

What Can Feng-Shui Do For You?
* Improve your Business
* Protect/Enhance your career
* Enhance Money
* Enhance Health
* Enhance Love, Romance, Marriage
* Baby birth date selection
* Name setup or correction for company/personal
* Illness Solution
* and more...

Please do not hesitate to contact Master Gan for an appointment.

regards,

Master Gan
International Destiny & Geomancy Consultant
Tel: +6014.6216.007
http://mastergan.weebly.com

Available in: Malaysia.Singapore.Taiwan.Hong
Kong.China.Thailand.Indonesia.Australia.Europe.USA.Dubai.India. 

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

[SPAM] I hope u open this! :)

------------------------------------------------------------------------------
Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM)
software. With Adobe AIR, Ajax developers can use existing skills and code to
build responsive, highly engaging applications that combine the power of local
resources and data with the reach of the web. Download the Adobe AIR SDK and
Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com

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

How to use" % signal change" option and the meaning of effect size

------------------------------------------------------------------------------
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H

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

ROI contour instead of a filled ROI

Dear experts,

Is there any option in marsbar that would convert a ROI  to a mask of  
the ROI's border with inside space filled with zeros?
If not, than maybe someone could share a piece of matlab code that can 
do it...

Thanks!

Victor

-- 

*********************************

Victor Vorobyev, Ph.D.

Centre for Cognitive Neuroscience
Department of Psychology
University of Turku
Assistentinkatu 7,
20014, Turku
Finland
*********************************

------------------------------------------------------------------------------
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H

Re: ROI contour instead of a filled ROI

Hi,

On Wed, Feb 18, 2009 at 7:15 AM, Victor Vorobyev <vicvor <at> utu.fi> wrote:
> Dear experts,
>
> Is there any option in marsbar that would convert a ROI  to a mask of
> the ROI's border with inside space filled with zeros?
> If not, than maybe someone could share a piece of matlab code that can
> do it...

Hmm - that would be a little complicated.  You could identify a voxel
in the middle of the ROI, then track paths away from the middle,
recording where the path crossed into 0s...    I haven't got any code
to hand to do that, but it wouldn't be very hard...

Best,

Matthew

------------------------------------------------------------------------------
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H

Re: How to use" % signal change" option and the meaning of effect size

Hi,

> First，when I do the statistic table, does the contrast value printed in the
> matlab window correspond to  the value of the beta in the contrast （for
> example，for a "1 0" contrast, the contrast value is the same as the first
> beta value of the model）?

Yes,

> And what does effect size mean?

Er - it's the usual SPM meaning - there are some emails on the SPM
list that might help.  It depends on the regressor and on the global
brain signal.  In some sense it's proportional to change relative to
the global brain signal as calculated by SPM.

> Second， How can I get the % signal change of one ROI (one subject)?  Do I
> need to import contrast firstly, and then click on the "% siganl change"?

You can only get percent signal change for events, not contrasts
(because you need the regressor corresponding to that event).    The
window allows you to select event types that you consider to be the
same, for that purpose, and for which you can then get a combined
percent change,

Best,

Matthew

------------------------------------------------------------------------------
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H
_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users

Re: [SPM] Marsbar error

Hi,

On Tue, Feb 17, 2009 at 4:18 AM, 이민혜 Lee, Minhye <gasifish <at> gmail.com> wrote:
> Whenever I try to use "Design" -> "set design from file" menu of Marsbar for
> ROI, it cannot find any mat.file which have been already made before by ROI
> definition menu.

The matlab GUI has some quirks in it in some versions.  Try typing in
the name of the file directly, in the GUI, if you know it's there.
Does that work?

Best,

Matthew

------------------------------------------------------------------------------
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H
_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users

extracting data using a variable for filenames

Hi All,

   When extracting data using user specified files (not from SPM design), is it
possible to specify the file names with a variable (either char or cell array?)
 This would be very helpful when extracting data from MANY files.

-josh

------------------------------------------------------------------------------
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H

Re: extracting data using a variable for filenames

Hi,

>   When extracting data using user specified files (not from SPM design), is it
> possible to specify the file names with a variable (either char or cell array?)
>  This would be very helpful when extracting data from MANY files.

In the GUI, SPM has an 'edit' button somewhere, you can paste in the
filenames there.

Batch is the most obvious way to go though...

Best,

Matthew

------------------------------------------------------------------------------
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H