[Homer-users] Using Matlab to substract conditions for ROI

[Chris Soraghan NUIM]

  -----Original Message-----
  From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvard.edu]On Behalf Of Theodore Huppert
  Sent: 22 August 2007 14:33
  To: homer-users at nmr.mgh.harvard.edu
  Subject: Re: [Homer-users] Using Matlab to substract conditions for ROI


  Felix-


     I tried to repeat the steps you had done, but I was unable to reproduce the error. I would be happy to take a look at the data file if you wish to send me (thuppert at nmr.mgh.harvard.edu) the *.hmr saved data file.  I can see if I can track down and fix any errors.  


  Also,note that the analysis in HOMER is done at three levels: i) individual scans ii) scan sessions and iii) multiple scans/subjects.  The "AVERAGE" button computes the average across only a single scan (level i).  The "AVERAGE ALL" button computes the average across a single session (level ii).  The ROI average button computes TWO the region-of-interest averages for the roi in level II and the group average (level III).  These should be stored in the *.hmr file as DO {idx}.ROI for level 2 and DOT{idx}.ROIavg for level 3.    If you want an ROI average PER condition, you should put each condition into a seperate "Session" (level 2 analysis).  Otherwise, the average will be computed across all the files.  A seperate MeasurementList can be specified for each condition (to my knowledge this works... it worked for me just now let me know if you find otherwise).  


  Note, there is also a way to specifiy more then 1 condition within a single file.  In the *.nirs files, the stimulus timing is specified by the variable "s".  This is typically a vector of 0's and 1's marking the onsets of the stimuli  (or it can be a recorded signal and HOMER will do some rising edge detection to find the onsets).  However, this variable (s) can also be a matrix, where each column specifies a different stimulus condition.  I.e. s(:,1) for condition 1, s(:,2) for condtion 2, etc.  Once loaded into HOMER, these additional conditions an be added to the linear model using the "Averaging Options" button and adding these conditions as regressors.  This is also how physiology measures can be added as regressors to the model.  See the sample file named "PhysiologyPhantom.nirs" for an example. 


  -Ted


  Theodore Huppert, Ph.D.
  thuppert at nmr.mgh.harvard.edu








  On Aug 21, 2007, at 1:31 PM, 李振国 wrote:


    hello,
    Thanks for your letter, I didn't have the case like this ,sorry!
    thank you
    guozi li



    在2007-08-21，"Felix Le" <> 写道：


      Hi, 
       
      I've done all the steps required to analyse an ROI and saved different files for each condition I want to analyze. But when I open the files in Matlab, I only get data average (AvgC) in the DataAvg section. When I go in the ROI section, the AvgC matrix is full of 0 and -0, wich is weird.
       
      Can I use the DataAvg for my substractions based on the specific MeasListAct I've set up ?
       
      Thank you, 
       
      Felix 


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