Katie

On Tue, Dec 7, 2010 at 4:16 PM, Douglas N Greve <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>> 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>.

>> >> >> >> >> >> >>
/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>>> 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>
<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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Phone Number: 617-724-2358 Fax: 617-726-7422

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MGH-NMR Center
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Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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