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Pierre Boveroux | 2 Apr 02:37
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Scale grand mean = 0 in a script

Hi,

I try to make a script to avoid thousand repetitive operations.
I use this script:

spm_name = ('my path\SPM.mat');
roi_file = ('my path\my roi file');
 
% Make marsbar design object
D = mardo(spm_name);

% Make marsbar ROI object
R = maroi(roi_file);

% Fetch data into marsbar data object
Y = get_marsy(R, D, 'mean' );

% get summary time course(s)
y = summary_data(Y);

save('my path\my file.txt', '-ascii', 'y');

This script works like if I did it with the GUI using
Extract ROI data (default)

But I need to use the Extract ROI data (full options)

With the GUI, I use to go into data, extract ROI data (full options), I chose my roi file, yes (use SPM design), SPM design (image from), scaling from RAW data, Scale grand mean to 0

I would like to find a script for the
Extract ROI data (full options) because I need to the Scale grand mean to be at 0.

I cannot find any help on the FAQ and trough the web, that's why I post this email.

I hope there is a solution ;-)

Thanks for your help

Kenpatchi76


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Bronwyn Glaser | 6 Apr 10:40
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Multiple contrast values

Hello,
Using the batch model, the run_tutorial, and the archives from this list, I have been trying to put together a batch script to extract data from 16 ROIs using data from 50 subjects. However, I am getting stuck on how to generate results for all 6 contrasts that I need to test for each ROI. While the script accepts 6 "add_contrasts", the results are always the values from the "effects of interest" contrast.

How can I change this code to get results back from all 6 contrasts, including the beta estimates for the voxels in the ROI ?

Here's an example of the bottom line of the output that comes back every time:

Contrast name                   ROI name:       Extra SS:    F statistic:  Uncorrected P:    Corrected P
--------------------------------------------------------------------------------------------------------

effects of interest
------------------------------------------
                                                                                                                                                    
              ROI:          14.04:           4.73:       0.000001:       0.000001


And here is the code: The part that comes before is identical to the batch model:

% Fetch data into marsbar data object
Y = get_marsy(R, D, 'mean');

% Estimate design on ROI data
E = estimate(D, Y);

% get design betas
b = betas(E); 

% %Set contrasts to design & Add contrasts, the first 6 columns are my conditions of interest, the next 6 are the rp movement regressors (added in SPM), and the last column represents a constant. Matlab would not accept them unless all 13 columns were represented
[E contrast_1] = add_contrasts(E, 'FL_HL', 'T', [0 0 1 0 -1 0 0 0 0 0 0 0 0]);
[E contrast_2] = add_contrasts(E, 'FP_HP', 'T', [0 0 0 1 0 -1 0 0 0 0 0 0 0]);
[E contrast_3] = add_contrasts(E, 'BL_HL', 'T', [1 0 0 0 -1 0 0 0 0 0 0 0 0]);
[E contrast_4] = add_contrasts(E, 'BP_HP', 'T', [0 1 0 0 0 -1 0 0 0 0 0 0 0]);
[E contrast_5] = add_contrasts(E, 'HL_AllL', 'T', [-1 0 -1 0 2 0 0 0 0 0 0 0 0]);
[E contrast_6] = add_contrasts(E, 'HP_AllP', 'T', [0 -1 0 -1 0 2 0 0 0 0 0 0 0]);

%Get and store statistics
stat_struct_1 = compute_contrasts(E, contrast_1);
stat_struct_2 = compute_contrasts(E, contrast_2);
stat_struct_3 = compute_contrasts(E, contrast_3);
stat_struct_4 = compute_contrasts(E, contrast_4);
stat_struct_5 = compute_contrasts(E, contrast_5);
stat_struct_6 = compute_contrasts(E, contrast_6);

[rep_strs, marsS, marsD, changef] = stat_table(E, 1:length(xCon))
disp(char(rep_strs))

savestruct(E, roi_file);


Thanks in advance!





                   

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Matthew Brett | 6 Apr 19:22
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Re: Multiple contrast values

Hi,

> Here's an example of the bottom line of the output that comes back every
> time:
> Contrast name                   ROI name:       Extra SS:    F statistic:
>  Uncorrected P:    Corrected P
> --------------------------------------------------------------------------------------------------------
> effects of interest
> ------------------------------------------
...
> [rep_strs, marsS, marsD, changef] = stat_table(E, 1:length(xCon))

The code looks right to me.  But, where does 'xCon' come from in the
last line?  Is it possible this is the unmodified contrast structure,
and that you need the extra line:

xCon = get_contrasts(E);

above that?

Best,

Matthew

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Matthew Brett | 7 Apr 18:30
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Re: [SPM] marsbar ROI

Hi,

> i am attmepting to conduct a ROI using the marsbar toolbox and i have a
> question regarding the first step of running the analysis. i have
> constructed my images and now i want to conduct the analysis. when i click
> on the set design from file option in the marsbar gui, the screen takes me
> to my working directory. however, there are no files to select, the folder
> is empty. so i tried to change the settings at the bottom to eg: all files,
> but none of these allow any files to be displayed.

Marsbar will be looking for SPM.mat files defining the design.

There have been problems with some versions of the matlab file
selection GUI.  You could try starting matlab with and without the
java virtual machine to see if that makes a difference:

# with
matlab

# without
matlab -nojvm

Best,

Matthew

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KIDLAB | 7 Apr 19:21
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??? Index exceeds matrix dimensions


Hello all, I have already looked for solutions to this and tried the
'add/edit filter for FMRI design' change to the fmristat AR(2)- didn't work,
and then tried the link to a 'bug' but that link was bad (from 2005).  I am
doing FIR event time course and get this error:

??? Index exceeds matrix dimensions.

Error in ==> mardo_2.event_x_fir>sf_ones_ons at 93
  sf(ton(j),:) = sf(ton(j),:) + 1;

Error in ==> mardo_2.event_x_fir at 61
  U.u = sf_ones_ons(U, xBF, k);

Error in ==> mardo.event_fitted_fir at 121
    Xn          = event_x_fir(D, [s e]', bin_length, bin_no, opts);

Error in ==> marsbar at 1662
  tc{i} = event_fitted_fir(marsRes, ...

Error in ==> spm at 831
evalin('base',CBs{v-1})

??? Error using ==> spm('PopUpCB',gcbo)
Index exceeds matrix dimensions.

??? Error while evaluating uicontrol Callback

Does anyone know why it would only show up for a certain contrast and not
others in the same subject/run?
Thanks!
Emily
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spam_master | 7 Apr 19:39
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[Err] Marsbar-users Digest, Vol 33, Issue 2

Transmit Report:

lark <at> korea.ac.kr¿¡°Ô ¸ÞÀÏ ¹ß¼ÛÀ» 4¹ø ½ÃµµÇßÁö¸¸ ½ÇÆÐÇÏ¿´½À´Ï´Ù.
(½ÇÆÐ ÀÌÀ¯ : 554 Transaction failed. 451 Requested action aborted: User UnKnown
lark <at> korea.ac.kr *MDAUserContext::readFrom()(163.152.6.99))

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DATA reponse fail  :¼ö½Å ¸ÞÀÏ ¼­¹ö·ÎºÎÅÍ ¸Þ¼¼Áö ¼ö½Å ½ÇÆÐ
Attachment: message/delivery-status, 263 bytes
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From: Transmit Report: lark <at> korea.ac.kr¿¡°Ô ¸ÞÀÏ ¹ß¼ÛÀ» 4¹ø ½ÃµµÇßÁö¸¸ ½ÇÆÐÇÏ¿´½À´Ï´Ù. (½ÇÆÐ ÀÌÀ¯ : 554 Transaction failed. 451 Requested action aborted: User UnKnown lark <at> korea.ac.kr *MDAUserContext::readFrom()(163.152.6.99)) <Âü°í> ½ÇÆÐ ÀÌÀ¯¿¡ ´ëÇÑ ¼³¸í User unknown :¸ÞÀÏÀ» ¼ö½ÅÇÒ »ç¿ëÀÚ°¡ Á¸ÀçÇÏÁö ¾ÊÀ½ Socket connect fail:¼ö½Å ¸ÞÀÏ ¼­¹ö¿Í ¿¬°á ½ÇÆÐ DATA write fail :¼ö½Å ¸ÞÀÏ ¼­¹ö·Î ¸Þ¼¼Áö ¼Û½Å ½ÇÆÐ DATA reponse fail :¼ö½Å ¸ÞÀÏ ¼­¹ö·ÎºÎÅÍ ¸Þ¼¼Áö ¼ö½Å ½ÇÆÐ <marsbar-users-request <at> lists.sourceforge.net>
Subject: Marsbar-users Digest, Vol 33, Issue 2
Date: 2009-04-07 17:21:19 GMT
Send Marsbar-users mailing list submissions to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

   1. [SPAM] [Err] Marsbar-users Digest, Vol 33, Issue 1
      (spam_master <at> korea.ac.kr)
   2. Multiple contrast values (Bronwyn Glaser)
   3. Re: Multiple contrast values (Matthew Brett)
   4. Re: [SPM] marsbar ROI (Matthew Brett)
   5.  ??? Index exceeds matrix dimensions (KIDLAB)

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Message: 1
Date: Thu, 02 Apr 2009 09:56:15 +0900
From: spam_master <at> korea.ac.kr
Subject: [Marsbar-users] [SPAM] [Err] Marsbar-users Digest, Vol 33,
	Issue 1
To: marsbar-users <at> lists.sourceforge.net
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Transmit Report:

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Subject: Marsbar-users Digest, Vol 33, Issue 1
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------------------------------

Message: 2
Date: Mon, 06 Apr 2009 10:40:53 +0200
From: Bronwyn Glaser <Bronwyn.Glaser <at> unige.ch>
Subject: [Marsbar-users] Multiple contrast values
To: marsbar-users <at> lists.sourceforge.net
Message-ID: <0BD6E4D3-3837-4838-8FB2-65830F4F031B <at> unige.ch>
Content-Type: text/plain; charset="us-ascii"

Hello,
Using the batch model, the run_tutorial, and the archives from this  
list, I have been trying to put together a batch script to extract  
data from 16 ROIs using data from 50 subjects. However, I am getting  
stuck on how to generate results for all 6 contrasts that I need to  
test for each ROI. While the script accepts 6 "add_contrasts", the  
results are always the values from the "effects of interest" contrast.

How can I change this code to get results back from all 6 contrasts,  
including the beta estimates for the voxels in the ROI ?

Here's an example of the bottom line of the output that comes back  
every time:

Contrast name                   ROI name:       Extra SS:    F  
statistic:  Uncorrected P:    Corrected P
--------------------------------------------------------------------------------------------------------

effects of interest
------------------------------------------

               ROI:          14.04:           4.73:        
0.000001:       0.000001

And here is the code: The part that comes before is identical to the  
batch model:

% Fetch data into marsbar data object
Y = get_marsy(R, D, 'mean');

% Estimate design on ROI data
E = estimate(D, Y);

% get design betas
b = betas(E);

% %Set contrasts to design & Add contrasts, the first 6 columns are my  
conditions of interest, the next 6 are the rp movement regressors  
(added in SPM), and the last column represents a constant. Matlab  
would not accept them unless all 13 columns were represented
[E contrast_1] = add_contrasts(E, 'FL_HL', 'T', [0 0 1 0 -1 0 0 0 0 0  
0 0 0]);
[E contrast_2] = add_contrasts(E, 'FP_HP', 'T', [0 0 0 1 0 -1 0 0 0 0  
0 0 0]);
[E contrast_3] = add_contrasts(E, 'BL_HL', 'T', [1 0 0 0 -1 0 0 0 0 0  
0 0 0]);
[E contrast_4] = add_contrasts(E, 'BP_HP', 'T', [0 1 0 0 0 -1 0 0 0 0  
0 0 0]);
[E contrast_5] = add_contrasts(E, 'HL_AllL', 'T', [-1 0 -1 0 2 0 0 0 0  
0 0 0 0]);
[E contrast_6] = add_contrasts(E, 'HP_AllP', 'T', [0 -1 0 -1 0 2 0 0 0  
0 0 0 0]);

%Get and store statistics
stat_struct_1 = compute_contrasts(E, contrast_1);
stat_struct_2 = compute_contrasts(E, contrast_2);
stat_struct_3 = compute_contrasts(E, contrast_3);
stat_struct_4 = compute_contrasts(E, contrast_4);
stat_struct_5 = compute_contrasts(E, contrast_5);
stat_struct_6 = compute_contrasts(E, contrast_6);

[rep_strs, marsS, marsD, changef] = stat_table(E, 1:length(xCon))
disp(char(rep_strs))

savestruct(E, roi_file);

Thanks in advance!

-------------- next part --------------
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------------------------------

Message: 3
Date: Mon, 6 Apr 2009 10:22:11 -0700
From: Matthew Brett <matthew.brett <at> gmail.com>
Subject: Re: [Marsbar-users] Multiple contrast values
To: Bronwyn Glaser <Bronwyn.Glaser <at> unige.ch>
Cc: marsbar-users <at> lists.sourceforge.net
Message-ID:
	<1e2af89e0904061022g5f711b27pfeaecc22655c1186 <at> mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi,

> Here's an example of the bottom line of the output that comes back every
> time:
> Contrast name ? ? ? ? ? ? ? ? ? ROI name: ? ? ? Extra SS: ? ?F statistic:
> ?Uncorrected P: ? ?Corrected P
> --------------------------------------------------------------------------------------------------------
> effects of interest
> ------------------------------------------
...
> [rep_strs, marsS, marsD, changef] = stat_table(E, 1:length(xCon))

The code looks right to me.  But, where does 'xCon' come from in the
last line?  Is it possible this is the unmodified contrast structure,
and that you need the extra line:

xCon = get_contrasts(E);

above that?

Best,

Matthew

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

Message: 4
Date: Tue, 7 Apr 2009 09:30:17 -0700
From: Matthew Brett <matthew.brett <at> gmail.com>
Subject: Re: [Marsbar-users] [SPM] marsbar ROI
To: Jeffrey West <jwest <at> mprc.umaryland.edu>
Cc: "marsbar-users <at> lists.sourceforge.net"
	<marsbar-users <at> lists.sourceforge.net>, SPM <at> jiscmail.ac.uk
Message-ID:
	<1e2af89e0904070930j77f1f1b7x1c80c6f4bdc207a0 <at> mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi,

> i am attmepting to conduct a ROI using the marsbar toolbox and i have a
> question regarding the first step of running the analysis. i have
> constructed my images and now i want to conduct the analysis. when i click
> on the set design from file option in the marsbar gui, the screen takes me
> to my working directory. however, there are no files to select, the folder
> is empty. so i tried to change the settings at the bottom to eg: all files,
> but none of these allow any files to be displayed.

Marsbar will be looking for SPM.mat files defining the design.

There have been problems with some versions of the matlab file
selection GUI.  You could try starting matlab with and without the
java virtual machine to see if that makes a difference:

# with
matlab

# without
matlab -nojvm

Best,

Matthew

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

Message: 5
Date: Tue, 7 Apr 2009 10:21:09 -0700 (PDT)
From: KIDLAB <krasnowkidlab <at> gmail.com>
Subject: [Marsbar-users]  ??? Index exceeds matrix dimensions
To: marsbar-users <at> lists.sourceforge.net
Message-ID: <22934032.post <at> talk.nabble.com>
Content-Type: text/plain; charset=us-ascii

Hello all, I have already looked for solutions to this and tried the
'add/edit filter for FMRI design' change to the fmristat AR(2)- didn't work,
and then tried the link to a 'bug' but that link was bad (from 2005).  I am
doing FIR event time course and get this error:

??? Index exceeds matrix dimensions.

Error in ==> mardo_2.event_x_fir>sf_ones_ons at 93
  sf(ton(j),:) = sf(ton(j),:) + 1;

Error in ==> mardo_2.event_x_fir at 61
  U.u = sf_ones_ons(U, xBF, k);

Error in ==> mardo.event_fitted_fir at 121
    Xn          = event_x_fir(D, [s e]', bin_length, bin_no, opts);

Error in ==> marsbar at 1662
  tc{i} = event_fitted_fir(marsRes, ...

Error in ==> spm at 831
evalin('base',CBs{v-1})

??? Error using ==> spm('PopUpCB',gcbo)
Index exceeds matrix dimensions.

??? Error while evaluating uicontrol Callback

Does anyone know why it would only show up for a certain contrast and not
others in the same subject/run?
Thanks!
Emily
-- 
View this message in context: http://www.nabble.com/----Index-exceeds-matrix-dimensions-tp22934032p22934032.html
Sent from the MarsBaR mailing list archive at Nabble.com.

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

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Matthew Brett | 8 Apr 00:12
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Re: ??? Index exceeds matrix dimensions

Hi,

> Hello all, I have already looked for solutions to this and tried the
> 'add/edit filter for FMRI design' change to the fmristat AR(2)- didn't work,
> and then tried the link to a 'bug' but that link was bad (from 2005).  I am
> doing FIR event time course and get this error:

What are you doing precisely when you get this error?  How many
sessions have you got in your design?  Is it an SPM5 design or an SPM2
design?  If you load up the design in SPM and review it (review the
events for example) does it look OK?

Best,

Matthew

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lijuan zou | 9 Apr 10:54
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(no subject)



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key laboratory of Cognitive NeuroScience and Learning
BeiJing Normal University
BeiJing,China
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Matthew Brett | 10 Apr 02:22
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Re: [SPM] questions about marsbar ?

Hi,

> i am doing ROI analysis,i was wondering whether we should change the marsbar
> options about the signal value ,such as max, min,or absmax? when i do a
> block ROI analysis, i didn't change any options ,the %signal change includes
> both negative and positive value. when i do ER analysis, i choose working
> with events ,and the max. and then the %signal change is positive .so i am
> wondering if i have to change options about marsbar before i do block ROI
> analysis . and what's the meaning about %signal change ?even when it's
> negative.

The % change will be negative, when the estimated time course goes
more down than it goes up.  It means that the signal seems to go down
relative to baseline rather than up.

Imagine that the estimated response from your block is an inverted
HRF.  In that case, if you take the max, you'll get a small positive
value as the undershoot, now positive, follows the peak (which is
negative).    If you take the absmax, then you'll get the peak, but
the peak is of course negative.  That seems the right way round to
me...

Best,

Matthew

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lijuan zou | 10 Apr 03:20
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Re: [SPM] questions about marsbar ?



2009/4/10 Matthew Brett <matthew.brett <at> gmail.com>
Hi,Matthew
thanks for your detailed information.now i have little knowledge about the %signal change,as the mannual is quite simple. as your idea,either option is right ,yes?the difference among max,absmax and mean just response different explaination,yes ? if i choose max and the results between different conditions can support my hypothesis, it's ok ,yes ?
thanks again.
 
 


> i am doing ROI analysis,i was wondering whether we should change the marsbar
> options about the signal value ,such as max, min,or absmax? when i do a
> block ROI analysis, i didn't change any options ,the %signal change includes
> both negative and positive value. when i do ER analysis, i choose working
> with events ,and the max. and then the %signal change is positive .so i am
> wondering if i have to change options about marsbar before i do block ROI
> analysis . and what's the meaning about %signal change ?even when it's
> negative.

The % change will be negative, when the estimated time course goes
more down than it goes up.  It means that the signal seems to go down
relative to baseline rather than up.

Imagine that the estimated response from your block is an inverted
HRF.  In that case, if you take the max, you'll get a small positive
value as the undershoot, now positive, follows the peak (which is
negative).    If you take the absmax, then you'll get the peak, but
the peak is of course negative.  That seems the right way round to
me...

Best,

Matthew



--
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key laboratory of Cognitive NeuroScience and Learning
BeiJing Normal University
BeiJing,China
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