明宗 曾 | 1 Mar 10:40
Picon
Favicon

A question

Hello,

 

I am a new user of Marsbar and I have a rather stupid question. How can I get the anatomical ROIs provided by MarsBar for regions that were of interest but not identified in our whole-brain contrasts?

 

 

Thanks again,

Carlos

 

___________________________________________________
您的生活即時通 - 溝通、娛樂、生活、工作一次搞定!
http://messenger.yahoo.com.tw/

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users
Tineke Snijders | 1 Mar 11:14
Picon

Re: A question

Hi Carlos,

>  I am a new user of Marsbar and I have a rather stupid question. How

> can I get the anatomical ROIs provided by MarsBar for regions that

> were of interest but not identified in our whole-brain contrasts?

 

In the marsbar tutorial (e.g. http://marsbar.sourceforge.net/marsbar_tutorial.pdf) on page 30 and 31 youoll find information on running an analysis using a structural ROI.

On the download-page of marsbar the package pmarsbar AAL ROIsq contains the anatomically defined ROIs based on the Tzourio-Mazoyer paper of 2002.

 

 

Tineke

 

From: marsbar-users-bounces <at> lists.sourceforge.net [mailto:marsbar-users-bounces <at> lists.sourceforge.net] On Behalf Of ?? ?
Sent: Thursday, March 01, 2007 10:41 AM
To: marsbar-users <at> lists.sourceforge.net
Subject: [Marsbar-users] A question

 

Hello,

 

I am a new user of Marsbar and I have a rather stupid question. How can I get the anatomical ROIs provided by MarsBar for regions that were of interest but not identified in our whole-brain contrasts?

 

 

Thanks again,

Carlos

 

 ___________________________________________________


-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users
Picon

Importing image ROIs

Hello,

I am a new user of MarsBar.
I would like to use it to make analyses using structural ROIs.
I have ready segmentations which I've obtained through a software I
developed  some years ago (called NeuroLine).
The segmentation results are saved in 3D labeled images. Each voxel is
associated with an integer value, that corresponds to one of the regions).
However, I am not having succes to use this images as entrance to MarsBar.
I've tried two options: to make them binary and to use the option "Build"
or to use the labeled images using the option "Import".
But a error message is returned: "Error reading information on: ...
filename.... please check that is in the correct form."
I've tried to create images in matlab with the same dimensions of the
available templates in AAL directory (just for test), but it resulted in
the same error. What could I make to solve my problem?
Is there any documentation that I could read about the importation of
structural ROIs?

Thank you very much for the attention.

Jane Maryam Rondina
State University of Campinas
Brazil.

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
Ninad Gujar | 1 Mar 22:43
Picon

Extract PSTH values

Dear Experts,

I read the marsbar FAQ and some messages on the archives about extracting FIR time course.

If i try doing it using the GUI method:

ROI definition -> Get SPM cluster(s)-> Write ROI(s) -> Write one cluster ->
Data -> Extract ROI data (default) -> Data -> Plot data (full) -> Type of
plot -> Time course. Now I have the graph.

I tried typing in whos at the Matlab command prompt and it gave me the following:

  Name       Size                    Bytes  Class

  SPM        1x1                  12311490  struct array
  ans        1x1                   5189430  marsy object
  hReg       1x1                         8  double array
  xSPM       1x1                    890488  struct array

Grand total is 1586948 elements using 18391416 bytes

How do I get these values ?

Also, what happens if for a particular subject for the selected ROI the activated voxels do not exist. (I was planning to use the batch script approach later on hence the doubt)

Thanks,

Ninad

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users
romain valabregue | 2 Mar 10:32
Picon

Transform roi defined in the normalized space into the native space

Dear Marsbar user

I would like to transform a roi previously definied in the normalized 
space into the native space
of a particular volume (from which I have estimated the normalisation 
using spm5 segmentation).

A first solution I can imagine is to transform the roi in an image. Then 
apply the inverse normalization
with spm (write normalize) by using the _seg_inv_sn.mat produce by the 
segmentation (in spm5).
And finally rebuild a roi from the transformed image.

This certainly not the optimal way. So I wonder if any one knows a more 
direct way to apply an estimated warps
to an roi ?

Thank for your help, (and for making marsbar compatible with spm5)

Chears

Romain

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
Roman Rodionov | 7 Mar 20:56
Picon
Favicon

getting adjusted response

Dear Matthew and users of MarsBar,

I need to calculate adjusted response in my batch.
I found mars_spm_graph which does this. It contains some GUI features asking about types of plots to draw. The workaround to avoid those to appear on the screen is obvious - change code of mars_spm_graph. It is not nice.
It would be nice to call spm_graph directly. My question is:
How can I change MarsBar structures in order to give them as parameters to spm_graph?
In other words: What is a solution to deal with different interfaces of spm_graph and mars_spm_graph?

Thanks in advance.
Roman

Never miss an email again!
Yahoo! Toolbar
alerts you the instant new Mail arrives. Check it out.
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users
Roman Rodionov | 7 Mar 21:03
Picon
Favicon

getting adjusted response

Dear Matthew and users of MarsBar,

I need to calculate adjusted response in my batch.
I found mars_spm_graph which does this. It contains some GUI features
asking about types of plots to draw. The workaround to avoid those to
appear on the screen is obvious - change code of mars_spm_graph. It is
not nice.
It would be nice to call spm_graph directly. My question is:
How can I change MarsBar structures in order to give them as parameters
to spm_graph?
In other words: What is a solution to deal with different interfaces of
spm_graph and mars_spm_graph?

Thanks in advance.
Roman

Expecting? Get great news right away with email Auto-Check.
Try the Yahoo! Mail Beta.
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users
Ninad Gujar | 7 Mar 22:12
Picon

PSTH

Hi Matthew,

Could anyone explain/elaborate on the steps reqd. to run via the GUI the process to extract the FIR (PSTH) time courses from the design ?

Thanks,

Ninad

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Marsbar-users mailing list
Marsbar-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/marsbar-users
Jim Lee | 8 Mar 18:29
Picon

Convolve with hrf


I have extracted signals from regions of interest that I want to low
pass filter by convolving with the hrf in SPM.xBF.bf. How do I scale the
hrf correctly in amplitude, and match the time scales of the signal (TR
seconds per point) and the hrf (0.1375 seconds per point).

Many Thanks in advance

Jim Lee

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
Matthew Brett | 8 Mar 19:58
Picon
Gravatar

Re: Convolve with hrf

Hi,

> I have extracted signals from regions of interest that I want to low
> pass filter by convolving with the hrf in SPM.xBF.bf. How do I scale the
> hrf correctly in amplitude, and match the time scales of the signal (TR
> seconds per point) and the hrf (0.1375 seconds per point).

What do you mean by scaling the hrf correctly?  I wasn't sure.

Convolving - you will need to resample the basis function at the
correct time bins.  Usually the xBF.bf field has 16 values for every
TR - if you have the default reference slice (1), then you can just
take every 16th value from the bf and convolve with that:

hrf = SPM.xB.bf(1:16:end);
lp_time_series = conv(time_series, hrf);

You might want to chop off the convolution run-out after that:

lp_time_series(end-len(hrf):end) = [];

Best,

Matthew

-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV

Gmane