MarsBaR ROI toolbox mailing list ()

明宗曾 | 1 Mar 10:40

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

headers

Tineke Snijders | 1 Mar 11:14

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

headers

Jane Maryam Rondina | 1 Mar 20:28

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

headers

Ninad Gujar | 1 Mar 22:43

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

headers

romain valabregue | 2 Mar 10:32

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

headers

Roman Rodionov | 7 Mar 20:56

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

headers

Roman Rodionov | 7 Mar 21:03

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

headers

Ninad Gujar | 7 Mar 22:12

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

headers

Jim Lee | 8 Mar 18:29

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

headers

Matthew Brett | 8 Mar 19:58

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

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

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	31