MarsBaR ROI toolbox mailing list ()

RRoman | 1 Oct 19:12

voxel-wise residuals


Dear Matthew,

Extracting mean residual for an ROI:
...
r=residuals(E);
ts=summary_data(r);

Could you please help me to find the way to obtain timeseries for each voxel
in the ROI.

Thanks,
Roman
--

-- 
View this message in context: http://www.nabble.com/voxel-wise-residuals-tp25703006p25703006.html
Sent from the MarsBaR mailing list archive at Nabble.com.

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
http://p.sf.net/sfu/devconf

headers

Matthew Brett | 1 Oct 22:54

Re: voxel-wise residuals

Hi,

> r=residuals(E);
> ts=summary_data(r);
>
> Could you please help me to find the way to obtain timeseries for each voxel
> in the ROI.

You mean, of the residuals?   That's a bit difficult, because the
estimation was on the summary time course, so there is only one set of
residuals - that from the summary time course.

You could try estimating on all the time courses in the ROI, as if
they were separate regions, instead of the summary data...  I can send
some code if that's what you mean.

Best,

Matthew

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
http://p.sf.net/sfu/devconf

headers

RRoman | 1 Oct 23:31

Re: voxel-wise residuals


>> r=residuals(E);
>> ts=summary_data(r);
>>
>> Could you please help me to find the way to obtain timeseries for each
>> voxel
>> in the ROI.
>
>You mean, of the residuals?  

yes

> That's a bit difficult, because the
>estimation was on the summary time course, so there is only one set of
>residuals - that from the summary time course.

this is the bit which I was missing. Thank you for explaining. I should have
guessed based on the speed of the calculation.

>You could try estimating on all the time courses in the ROI, as if
>they were separate regions, instead of the summary data...  I can send
>some code if that's what you mean.

Thank you very much for offering your help. I appreciate that. 
I'll give it a try and ask you if fail.

Best,
Roman
--

-- 
View this message in context: http://www.nabble.com/voxel-wise-residuals-tp25703006p25706869.html

(Continue reading)

headers

Matthew Brett | 2 Oct 00:01

Re: [SPM] 'draw' function in marsbar

Hi,

> I am wanting to use marsbar to draw an ROI, but contrary to what it says
> here:
> http://marsbar.sourceforge.net/tutorial/define.html
> and in the pdf documentation, I don't see a 'draw' option under the marsbar
> dropdown menu.  Am I looking in the wrong place?

I've Cc'ed the marsbar list - that's the best list for marsbar questions.

Thanks for letting me know about this - I removed the ROI drawing some
time ago but hadn't changed the documentation - I will fix that.
Something like MRIcron is good for drawing - you then need to import
the ROI into marsbar format using ROI definition -> import.

Sorry about that,

 Best,

Matthew

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
http://p.sf.net/sfu/devconf

headers

Steffie Nelson | 3 Oct 23:38

How many voxels in the cluster I've chosen?

Hi Matthew,

Perhaps I’ve missed this somewhere in the display, but when I go to view an ROI I can’t find anywhere that indicates how many voxels are in the ROI cluster that I’ve selected. If it isn’t showing up in the GUI, is there another way to get this information?

Also, I work with mostly un-normalized data, so I’d like to change the image that the ROIs are projected upon. However, when I go to Options, Edit Options, Defaults area, and select ‘Default Structurals’ I get an error that I think has something to do with a getfile function. I’m using SPM8.

Any input would be greatly appreciated. Aside from these minor hiccups, I’m a big fan of your program.

Cheers,

Steffie Nelson
Graduate Student
Eagleman Lab
Department of Neuroscience
Baylor College of Medicine
One Baylor Plaza Houston 77030

p: 713-798-6224 f: 713-798-4488

snelson <at> bcm.edu
www.synesthete.org

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
http://p.sf.net/sfu/devconf

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

headers

tony han | 6 Oct 06:05

run_preprocess error

Dear all,
I just start to use marsbar and installed it with spm5 in Matlab R2008a. As I use run_preprocess to process the example data sesssion 2, errors occur as follows:

??? Attempted to access condons(:,2); index out of bounds because size(condons)=[0,0].
Error in ==> er_model_spm2 at 88
tmp = condons(:,2); % get stimulus column
Error in ==> configure_er_model at 74
er_model_spm2(sess_dir, sesses, ana_dir);
Error in ==> run_preprocess at 25
model_file = configure_er_model(subjroot, sesses{ss}, sdirname);

So how should I solve this problem?
Many thanks!
Tony

Hotmail: Trusted email with powerful SPAM protection. Sign up now.

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
http://p.sf.net/sfu/devconf

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

headers

tony han | 6 Oct 06:23

starting problem

Dear all,
Sorry for another problem I have when starting marsbar. Previously I use marsbar with spm5 in Matlab 7.1. Now I update the Matlab to R2008a, but same problem occurs as follows:

>> marsbar
MarsBaR analysis functions prepended to path
Warning: In the directory "E:\Program Files\MATLAB\R2008a\toolbox\spm5", file2mat.mexw32 now shadows
file2mat.dll.
Please see the MATLAB 7.1 Release Notes.
> In nifti.subsref>rec at 219
In nifti.subsref at 45
In spm_vol_nifti at 19
In spm_vol>subfunc at 139
In spm_vol>subfunc1 at 87
In spm_vol>subfunc2 at 73
In spm_vol at 57
In mars_space.mars_space at 37
In mars_options at 41
In marsbar at 163
In marsbar at 57
Loaded MarsBaR defaults from base defaults

What's wrong with that? Thanks for your help!

Tony

Hotmail: Powerful Free email with security by Microsoft. Get it now.

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
http://p.sf.net/sfu/devconf

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

headers

Matthew Brett | 6 Oct 11:16

Re: run_preprocess error

Hi,

On Tue, Oct 6, 2009 at 5:05 AM, tony han <oktonyhan <at> hotmail.com> wrote:
> Dear all,
>    I just start to use marsbar and installed it with spm5 in Matlab R2008a.
> As I use run_preprocess to process the example data sesssion 2, errors occur
> as follows:
>
> ??? Attempted to access condons(:,2); index out of bounds because
> size(condons)=[0,0].
> Error in ==> er_model_spm2 at 88
>   tmp = condons(:,2); % get stimulus column
> Error in ==> configure_er_model at 74
>   er_model_spm2(sess_dir, sesses, ana_dir);
> Error in ==> run_preprocess at 25
>   model_file = configure_er_model(subjroot, sesses{ss}, sdirname);

It looks like the script is not finding the conditions files where it
was expecting them.  Are you sure that you specified the path to the
data correctly (you might try setting the data path at the top of the
run_preprocess script).  Some dearchivers on windows wipe out the path
components - could you try downloading the .zip version of the example
data and unpacking that, making sure the paths are also extracted.
Does that work?

Best,

Matthew

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
http://p.sf.net/sfu/devconf

headers

Matthew Brett | 6 Oct 11:18

Re: starting problem

Hi,

> MarsBaR analysis functions prepended to path
> Warning: In the directory "E:\Program Files\MATLAB\R2008a\toolbox\spm5",
> file2mat.mexw32 now shadows
> file2mat.dll.

I think this is a benign warning caused by an older and more recent
compiled SPM routine in the same directory...

Best,

Matthew

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
http://p.sf.net/sfu/devconf

headers

Scott Fairhall | 9 Oct 23:34

Nutty F-values

Dear All,

I’ve been using marsbar now for quite a few years and over this time I have occasionally run into some rather striking anomalies between the T and F values that I get for my ROIs (for example, a T of 2.5 and an F of 125 for an equivalent contrast [i.e. 1 1 -1 -1]). In this case the F-test should have a p value twice that of the one-tailed T-test.
I’ve never been able to isolate exactly what’s causing this. It has popped up in a number of apparently random ROIs, contrasts and studies and recently a student has had the same issue. It is clearly a problem with the F value (these are reasonably tight comparisons, F sometimes shoots up above 300 and the T values correspond to the whole brain SPM).
Would anyone have any ideas what might be causing this?

All the best,

Scott Fairhall
Dept of Psychology
Harvard University
William James Building, rm 910.
Cambridge, MA

------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay 
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference

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

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