It comes down to whether you think there will be 0 activation in this area if there are 0 items held in memory. If so, then what you have is fine.
doug
Katie Bettencourt wrote:
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 <mailto: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><mailto: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>><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 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>
<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>>><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:
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>>>
<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>
<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>>
<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
greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
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MGH-NMR Center
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