Print

---

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
>>>
>>
>>
>