I'm not sure if that's exactly what I am saying.  Basically, there is an area in the brain (which I am trying to localize) that tracks the number of items you are holding in memory so that the more items you hold in memory, the higher the bold activation.  We have behavioral results saying how many items people are holding in each of the conditions, and we want to use this to get out an area in which the BOLD activation mirrors this.  In Brain Voyager, this is done by weighting the conditions by the behavior, which is what I am trying to do here.  I'm not sure that that translates exactly into what you are saying.

Katie

On Wed, Dec 8, 2010 at 11:47 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

It depends on what you want to test exactly.  You can just weight each presentation and test against fixation as you suggest. This implies that the response amp is 0 when your weight is 0. If that's not the case, then you need to make a modification. Let me know if  you need that.

doug

Katie Bettencourt wrote:
Ah, there was one condition (the throw away one) that was all weighted 0, I will just change the weight on that one back to 1.  For looking at what shows up in the weighted analysis, if I want to see areas that increase along my weights, would I just make a contrast of all of them vs fixation, and then any area that shows up in that comparison would be an area that followed my weighting (if that makes sense)?

Katie

On Tue, Dec 7, 2010 at 4:16 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   They do not need to be whole numbers. 0s should be ok, unless
   there are some conditions that only have 0 weighting. For throw
   aways conditions, you usually just create a separate condition and
   leave the weight at 1.

   Katie Bettencourt wrote:

       It does run ok when the FIR is all weighted to 1.  There are
       weights of 0 for the couple conditions that were essentially
       throwaway trials for counterbalancing reasons.  Is that what
       is causing the trouble?  Do the numbers need to be whole numbers?

       katie

       On Tue, Dec 7, 2010 at 3:23 PM, Douglas N Greve
       <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
       <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

          It should work in 4.5 too. The numbers are weights. So if  you
          think that the response to presentation A of condition 1
       will be
          twice that of presentation B of condition 1, then you would
       have a
          weight of 2 for pres A and 1 for pres B. The weight of fixation
          (condition 0) is unimportant. I can't tell from the error msg
          below whether the error is caused by the weighting or by
       the FIR.
          Does the FIR run ok when it is not weighted? Are there any task
          weights that are 0?

          doug

          Katie Bettencourt wrote:

              Ah, what I want is the 2nd one then.  I was trying to
       do this
              in freesurfer v 4.5 but I can't figure out how to use
       the 4th
              column in a way that doesn't crash during selxavg3-sess and
              there isn't much on the wiki about how to use it, what
       sorts
              of numbers are acceptable in the 4th column?  I have 6
              conditions plus fixation.  one condition I want to be
       ignored
              (so I set the weight to 0), and then I want an increase
       as set
              size increases but with a plateau at large set sizes.
        I tried
              weighting them as whole numbers above 1 (which was what
              fixation was set to), weighing them as all less than 1 (but
              with fixation still as 1), weighing them less than 1 and so
              that combined they add up to 1 (fixation still as 1),
       but all
              errored our in selxavg3-sess.  the same data analyzes fine
              unweighted (all 1s in the 4th column of the paradigm file).

              This is the output I get when I try to change the 4th
       column
              of the paradigm file:

              selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis
              supIPS-fir-weighted -overwrite
                     --------------------------------------------------------------
              selxavg3-sess logfile is
                     /home/kcb/mri-space/supIPS_loc/log/selxavg3-sess-bold-supIPS-fir-weighted-101207145505.log
                     --------------------------------------------------------------
              -------------------------------------------
              /home/kcb/mri-space/101103TM_supIPS
              Tue Dec  7 14:55:05 EST 2010
              anadir =
                     /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted
              analysis supIPS-fir-weighted alread exists for
       101103TM_supIPS
               ... reanalyzing (deleting old analysis)
              ------------------------------------------
              ------- matlab output --------------------
              Warning: Unable to open display 'iconic'.  You will not be
              able to display graphics on the screen.

                                         < M A T L A B (R) >
                               Copyright 1984-2010 The MathWorks, Inc.
                             Version 7.10.0.499 (R2010a) 64-bit (glnxa64)
                                           February 5, 2010

                To get started, type one of these: helpwin, helpdesk,
       or demo.
               For product information, visit www.mathworks.com
       <http://www.mathworks.com>
              <http://www.mathworks.com> <http://www.mathworks.com>.


               >> >> >> >> >> >> >>
              /usr/local/freesurfer4.5/fsfast/toolbox/fast_selxavg3.m
              >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
              $Id: fast_selxavg3.m,v 1.55.2.8 2009/04/17 20:09:46
       greve Exp $
              outtop = /home/kcb/mri-space
              Extension format = nii
              UseFloat = 0
              INFO: mask is not set, setting to brain
               1 act_vs_fix-delay.mat
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Excluding 2 points
              nruns = 2
              autostimdur = 0


              outanadir =
                     /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted
              Found 48212/124416 (38.8) voxels in mask
              Creating Design Matrix
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Excluding 2 points
              Warning: Matrix is singular to working precision.
              > In fast_selxavg3 at 212
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Ignoring stimulus duration for FIR model
              Excluding 2 points
              Warning: Matrix is singular to working precision.
              > In fast_selxavg3 at 212
              ntptot = 616, nX = 80, DOF = 536
              Saving X matrix to
                     /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted/Xtmp.mat
              ??? Error using ==> svd
              Input to SVD must not contain NaN or Inf.

              Error in ==> cond at 40
                s = svd(A);

              Error in ==> fast_selxavg3 at 248
               XCond = cond(XtX);
               >> ------------------------------------------
              ERROR: fast_selxavg3() failed\n




              katie

              On Tue, Dec 7, 2010 at 2:50 PM, Douglas N Greve
              <greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>
       <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>>
              <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>
              <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:

                 what are you trying to do exactly? The external
       regressor is
                 usually used with a continuous measure (eg, skin
              conductance, it
                 can also be used to seed-based functional
       connectivity). If you
                 expect the hemodynamic response to be scaled by
       something (eg,
                 reaction time), then that should be incorporated
       into the
              paradigm
                 file in the 4th column.

                 doug

                 Katie Bettencourt wrote:

                     So I just need 1 column with a line for each
       time point
              that
                     has the weight I want to give the condition that is
              occuring
                     at that time point?  And what do you mean a
       contrast will
                     automatically be created for it?  I was trying
       to use
              this to
                     find an area that increases with load but then
       plateaus
              at a
                     point where subject's behavioral performance
       plateaus (so
                     essentially looking for a mirroring of the
       behavioral
              data in
                     the neural data), will there just be a contrast
       created
              after
                     I run selxavg3-sess that I can bring up with
       tksurfer-sess
                     afterwards?

                     katie

                     On Tue, Dec 7, 2010 at 11:40 AM, Douglas N Greve
                     <greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>
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              <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>>>
                     <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>
              <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>>
                     <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>
              <mailto:greve@nmr.mgh.harvard.edu
       <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:

                        It is just a text file with a value for each
       time point.
                     You can
                        have multiple columns, but if it is a task,
       then you
                     probably want
                        to keep one to make the interpretation easier. A
              contrast will
                        automatically be created for it. You can look
       at the
              mcprextreg
                        file created by the motion correction to get
       an idea.

                        doug

                        Katie Bettencourt wrote:

                            I'm trying to set up an analysis using an
       external
                     regressor
                            (as part of the mkanalysis-sess stream,
       -taskreg
              flag)  in
                            version 5, but I'm not sure what the
       taskreg.dat
              file
                     should
                            look like.  The only thing I can find is
       that it
              should
                     have a
                            line for each time point.  Does anyone
       have any more
                     guidance
                            than this?

                            Katie
                                                 ------------------------------------------------------------------------

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                        --     Douglas N. Greve, Ph.D.
                        MGH-NMR Center
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          --     Douglas N. Greve, Ph.D.
          MGH-NMR Center
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MGH-NMR Center
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