Aser,

The number of points in the the first level design are per volume. If you have 300 volumes, you get 300 PM values. If you use the fMRI data as the input into spm_summarise, then you will get 300 values for the BOLD values that can be plotted on the y-axis. If you look at the SPM.mat file in SPM.xX.X, you can get the 300 PM values that can be plotted on the x-axis. It doesn't matter that you specify you trials in seconds or scans.

To get the plotted values, you'll need to residual the PM and BOLD values using the rest of the design matrix.

Now, if you are wanting to plot each trial against the PM value, then that is different. To plot each trial, you need to follow the procedures for beta-series correlations - create a regressor for each trial. Then extract the amplitude of each trial. Then plot the amplitudes against the PM.

The two analysis are quite different. The former is based on the SPM output and are similar to the SPM plots. The latter requires a different analysis than what you have currently performed in SPM.

Hope this helps.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Sat, Feb 7, 2015 at 1:44 PM, Aser A <[log in to unmask]> wrote:
Hi Donald,

This did not work... The point I want is to extract the values that I get when I press "Plot parametric response". Because this plots them as they were specified in the first level design (i.e. not per volume). For example, if I specify the trials in seconds (and say I have 300 points), when I plot the parametric response it generates a plot like what I attached that has 300 points in the y axis which is the BOLD/PM and 300 points in the x axis which is the PM. So I just want to reach to the values in the plot.

Thanks



On Fri, Feb 6, 2015 at 5:29 PM, MCLAREN, Donald <[log in to unmask]> wrote:
Andy,

I believe that spm_summarise will work. This will allow you to get he BOLD data. The PM values can be extracted from SPM.xX.X.

function [Y, xY] = spm_summarise(V,xY,fhandle,keepNaNs)

% Summarise data within a Region of Interest

% FUNCTION [Y, xY] = spm_summarise(V,xY,fhandle)

% V       - [1 x n] vector of mapped image volumes to read (from spm_vol)

%           Or a char array of filenames

% xY      - VOI structure (from spm_ROI)

%           Or a VOI_*.mat (from spm_regions) or a mask image filename

%           Or the keyword 'all' to summarise all voxels in the images

%           Or a [3 x m] matrix of voxel coordinates {mm}

% fhandle - function handle to be applied on image data within VOI

%           Must transform a [1 x m] array into a [1 x p] array

%           Default is Identity (returns raw data, vectorised into rows).

%           Can also use keyword 'litres' to compute the total volume,

%           within the region of interest, for a tissue segment image.

%

% Y       - [n x p] data summary

% xY      - (updated) VOI structure

%__________________________________________________________________________

%

% Example:

% spm_summarise('beta_0001.nii',...

%               struct('def','sphere', 'spec',8, 'xyz',[10 20 30]'),...

%               @mean)

%__________________________________________________________________________

% Copyright (C) 2010-2012 Wellcome Trust Centre for Neuroimaging


% Guillaume Flandin, Ged Ridgway

% $Id: spm_summarise.m 5670 2013-10-04 16:48:38Z ged $


Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=====================
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.

On Fri, Feb 6, 2015 at 6:28 AM, fMRI <[log in to unmask]> wrote:
Hi Andy, 

I do not think that Matsbar is going to extract the values in the parametric response. I tried this but it did not work with me.

Regards,

AS

On 6 Feb 2015, at 00:59, Andy Yeung <[log in to unmask]> wrote:

Dear Aser,

ROI data can be extracted using Marsbar.
Another idea might be to extract first eigenvariate by drawing a sphere centred at your peak voxel.
Just some ideas, not sure if they help.

Best,
Andy

On Fri, Feb 6, 2015 at 7:39 AM, Aser A <[log in to unmask]> wrote:
Hello all,

Using SPM and parametric response, I can plot the response at each voxel where I get in the x axis the parametric modulation values and the y axis the BOLD/PM. If I would like to plot the response in a ROI, I do not think that I can do this directly using SPM. 

So What I am trying to do is to extract the plotted values produced using the plot parametric response for several voxels. The only, I think simple, problem that I have is I cannot reach to the plotted values either in the x or y axis used by SPM to plot the PM ? If I find them then I can average the values of the y axis across several voxels. 

Can anyone help with this please ?


Many thanks

Adnan A