New subject: selxavg-sess vs selxavg3-sess

1 Dec 2010

      Hi all, I'm still trying to sort out some problems I've been having with
selxavg3-sess in Freesurfer 4.5 on RedHat Linux, CentOs 5.5.
I've tried a bunch of things, but I will provide the simplified process here
as a starting point.  I have a blocked design where I have 3 conditions,
fixation, noise, and shape.  Things look good when I compare shape vs noise,
but very very bad in an unrealistic way when I compare anything to fixation
(shape vs fixation, noise vs fixation, active vs fixation).  Attached are
the pictures I get.  The subjects are not moving much (checked the motion
correction output).  I tried running the analysis with the -no-whiten flag
and it made no difference.  When this data is analyzed with Brain Voyager by
others in my lab, this problem doesn't exist, and you see appropriate
activity for the vs. fixation conditions.  When I run data collected with
PACE, I don't have this comparison to fixation problem, but I do for nonPACE
bold runs.
Commands I ran:
 mkanalysis-sess -analysis infIPS -TR 2 -paradigm loc.dat -designtype
blocked -funcstem fmc -motioncor -runlistfile loc_runs.txt -inorm -nskip 2
-nconditions 2 -timewindow 20 -gammafit 2.25 1.25 -noautostimdur
mkcontrast-sess -analysis infIPS -contrast shape_vs_fix -a 2 -c 0
mkcontrast-sess -analysis infIPS -contrast noise_vs_fix -a 1 -c 0
mkcontrast-sess -analysis infIPS -contrast shape_vs_noise -a 2 -c 1
mkcontrast-sess -analysis infIPS -contrast act_vs_fix -a 2 -a 1 -c 0
selxavg3-sess -sf loc_loc-sess -df loc_loc.dir -analysis infIPS
Any thoughts?
Katie
On Fri, Nov 12, 2010 at 4:19 PM, Katie Bettencourt kcrum@bu.edu wrote:
...
This is in blocked designs and in event related gamma designs (I haven't
had time to finish sorting out my FIR problems, so that's a different
email), but they've all boiled down to essentially these sets of commands:
mkanalysis-sess.new -analysis num_loc -TR 2 -paradigm num.dat -designtype
blocked -funcstem fmc -runlistfile num_runs.txt -inorm -nconditions 4
-timewindow 20 -gammafit 2.25 1.25
mkcontrast-sess -analysis num_loc -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4
-c 0
mkcontrast-sess -analysis num_loc -contrast lnum_vs_snum -a 1 -c 2
...etc...
preproc-sess -nosmooth -sf num-sess -df num.dir
selxavg3-sess -sf num-sess -df num.dir -analysis num_loc -skip
-or-
selxavg-sess -sf num-sess -df num.dir -analysis num_loc
stxgrinder-sess -analysis num_loc -contrast [contrastname here] -sf
num-sess -df num.dir
I have tried running the same (w/ selxavg3-sess) as above but with using:

the -nskip 2 flag in mkanalysis-sess.new to skip the first 2 TRs (no

change)
2.  using mkanalysis-sess (no .new) with the -no-whiten flag
3.  getting rid of the -timewindow flag
4.  running stxgrinder-sess and paint-sess after selxavg3-sess to get the
sig-0-lh and sig-0-rh files
None of these things have had any effect.  I've checked the motion
parameters and they haven't moved much.  The raw data seems fine because it
analyzes fine in BrainVoyager (which I don't want to use for a multitude of
reasons, but others in my lab do use).  I still end up with the entire brain
activating and activating strongly for the baseline conditions, but only if
the data were acquired using nonPACE BOLD runs and only if I use
selxavg3-sess.  My PACE data is fine in both.
Katie
On Fri, Nov 12, 2010 at 3:29 PM, Douglas N Greve <
greve@nmr.mgh.harvard.edu> wrote:
...
And this is not usging FIR, right? Can you send me your mkanalysis-sess
commands for selxavg-sess and selxavg3-sess?
Katie Bettencourt wrote:
...
That's ok, we;ve gone back and forth a bit.
The real problem is that when I use selxavg3-sess on data collected in
non PACE sequences, it looks fine in contrasts that aren't against baseline
(the 0 condition in the paradigm files) but when I look at conditions vs
baseline (like act-vs-fix) the entire brain shows strong activation for the
baseline condition (I had attached pictures originally, but basically
imaging a brain that looks pretty much all blue and you get an accurate
picture).  When I used selxavg-sess instead, I see a little less activation
for the comparisons that aren't against baseline, but appropriate pictures
when I compare against baseline.
As I've said, this data has been analyzed in Brain voyager and looks fine
(actually stronger) but doesn't work in Freesurfer right.  The activity I
see with selxavg3-sess when I compare nonbaseline conditions (ie.
shape-vs-noise) appears to be in similar locations in both Freesurfer and
BrainVoyager (though again weaker in Freesurfer for same thresholds).  It's
really just the comparison to baseline that seems to be screwed up.
Katie
On Fri, Nov 12, 2010 at 3:11 PM, Douglas N Greve <
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
sorry, I've lost track of what the problem is exactly. If I
   remember: you analyze using selxavg-sess and brain voyager and
   things look ok, but in selxavg3-sess you lose activation?
doug
Katie Bettencourt wrote:
   I tried it with the -no-whiten flag and again there is no
   difference between the -no-whiten and the normal version.  Any
   other thoughts?  The only thing that seems to come up is that
   when the data is collected with a PACE sequence I don't get
   this problem, but a standard BOLD sequence does.  I would
   assume it was motion or something, but the motion parameters
   are small and the data works fine in brain voyager.

   The only thing I think that is done different in brain voyager
   is that they skip the first 2 TRs (and each experiment starts
   with fixation), I tried to do that with the -nskip 2 option,
   do I need to also use the -tpef function or is that only if
   your paradigm file doesn't start at 0?

   Katie

   On Fri, Nov 12, 2010 at 1:02 PM, Katie Bettencourt
   <kcrum@bu.edu <mailto:kcrum@bu.edu> <mailto:kcrum@bu.edu

   <mailto:kcrum@bu.edu>>> wrote:

      No, it was with .new  should I be using mkanalysis-sess usually
      instead of mkanalysis-sess.new?  What exactly is the
   difference?

      Katie

      On Fri, Nov 12, 2010 at 1:00 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:

          Is it in mkanalysis-sess (without the ".new")?

          Katie Bettencourt wrote:

              I tried using the no-whiten flag with
   mkanalysis.new and
              it said there was no such flag and I can't find any
              reference to it on the wiki.

              Katie

              On Wed, Nov 10, 2010 at 5:31 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:

                 Can you create a new analysis using the
   -no-whiten flag
              and re-run
                 selxavg3-sess? For the other error, you need to
   select
              a prestim
                 and timewindow that are integer multiples of 1.5.

                 doug

                 Katie Bettencourt wrote:

                     So this data has been previously analyzed in
              BrainVoyager, and
                     there is no problems with it, subject
   movement is
              very low (<
                     2mm across all runs and timepoints), though
   I did
              notice that
                     this problem does not happen when I analyze data
              collected
                     with PACE sequences, and not with ones that
   do not
              use PACE.
                      I tried running the selxavg3-sess with the
              -svres-unwhitened
                     (which is the only whitening related command I
              could see), but
                     it made no difference.  I'm not sure how to
   look at
              the raw
                     data precisely, but I do know it works
   correctly in BV.

                     Any other thoughts on what's going wrong
   here?  Can
              I at least
                     trust the data that isn't against baseline
   in this
              case?  It
                     looks similar, though weaker to the same data
              analyzed with
                     BrainVoyager (not sure why I keep getting weaker
              activation in
                     Freesurfer than Brainvoyager, but that's a
   different
                     consideration).

                     Somewhat relatedly, when I try to run a FIR
              analysis with
                     selxavg3-sess (instead of selxavg-sess):
                     mkanalysis-sess.new -analysis supIPS_loc-fir -TR
              1.5 -paradigm
                     supIPS.dat -designtype event-related
   -funcstem fmc
              -motioncor
                     -runlistfile supIPSruns.txt -inorm -nskip 2
              -nconditions 6
                     -tprestim 2 -timewindow 20

                     selxavg3-sess -s 101103TM -df supIPS.dir
   -analysis
              supIPS_loc-fir

                     I get this output/error:

                     selxavg3-sess logfile is

/home/kcb/mri-space/supIPS_loc/log/selxavg3-sess-bold-supIPS_loc-fir-101110150643.log

                     -------------------------------------------
                     /home/kcb/mri-space/101103TM_supIPS
                     Wed Nov 10 15:06:43 EST 2010
                     anadir =
              /home/kcb/mri-space/101103TM_supIPS/bold/supIPS_loc-fir
                     ------------------------------------------
                     ------- 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: acfbins is not set, setting to 10
                         INFO: mask is not set, setting to brain
                          1 1_vs_fix.mat
                          2 2_vs_1.mat
                          3 2_vs_fix.mat
                          4 3_vs_1.mat
                          5 3_vs_2.mat
                          6 3_vs_fix.mat
                          7 4_vs_1.mat
                          8 4_vs_2.mat
                          9 4_vs_3.mat
                         10 4_vs_fix.mat
                         11 643_vs_2-delay.mat
                         12 643_vs_2.mat
                         13 6_vs_1.mat
                         14 6_vs_2.mat
                         15 6_vs_3.mat
                         16 6_vs_4.mat
                         17 6_vs_fix.mat
                         18 act_vs_fix.mat
                         19 allvres.mat
                         20 omnibus.mat
                         21 zallvres.mat
                         22 zomnibus.mat
                         ERROR: psdmin=-2 not int mult of dpsd=1.5
                         ERROR: psdmax=17.5 not int mult of dpsd=1.5
                         ??? Index exceeds matrix dimensions.
                     Error in ==> fast_condctrstmtx at 102
                      Rpost  = diag(WDelays(nnpost)); % Diagonal
              PostStim Weights

                     Error in ==> flac_conmat at 64
                      R =

fast_condctrstmtx(dpsd,TW,-psdmin,con.sumevreg,WDelay,1);
                     Error in ==> fast_ldanaflac at 474
                      flactmp = flac_conmat(flac,nthcon);

                     Error in ==> fast_selxavg3 at 85
                      flac0 = fast_ldanaflac(analysis);
                      >> ------------------------------------------
                     ERROR: fast_selxavg3() failed\n

                     Katie

                     On Wed, Nov 10, 2010 at 11:03 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>>>>> wrote:

                        I have no idea what is happening, but I can
              suggest a few
                     checks. Have
                        you looked at the motion correction
   plots? Have
              you looked
                     at the raw
                        data? Another thing to try is to turn off
              whitening when
                     you make the
                        analysis for selxavg3-sess.

                        doug

                        Katie Bettencourt wrote:
                        > Hi all,
                        >
                        > I'm still trying to figure out what's
   going on
              with the
                     differences
                        > I'm getting between selxavg-sess and
              selxavg3-sess.  I"m
                     using
                        > freesurfer4.5. I was using
   selxavg3-sess (as
              suggested on
                     the wiki)
                        > but I was getting weird activation maps
   when I
              compared any
                        condition
                        > vs. baseline, where most of the brain
   was more
              activity
                     for baseline
                        > (which was fixation) - see the attached
              picture for
                        > act-fix-gamma-selxavg3-rh.png.   So I ran
              selxavg-sess
                     which was
                        what
                        > I used to run with an older version of
              freesurfer, and when I
                        did this
                        > I got a more appropriate picture - see
              act-fix-gamma-rh.png
                        >
                        > The experiment starts with fixation
   (baseline)
              so I tried
                        running the
                        > analysis with and without skipping the
   first 2
              TRs to account
                        for the
                        > BOLD spike, but it makes no difference
   in the
              activation map.
                        >
                        > These are essentially the commands I ran:
                        > mkanalysis-sess.new -analysis loc_loc -TR 2
              -paradigm loc.dat
                        > -designtype blocked -funcstem fmc
   -runlistfile
                     loc_runs.txt -inorm
                        > -nconditions 2 -timewindow 20 -gammafit
   2.25 1.25
                        >
                        > mkcontrast-sess -analysis loc_loc -contrast
              shape_vs_fix
                     -a 2 -c 0
                        >
                        > selxavg3-sess -s 101006SP_loc_loc -df
   loc_loc.dir
                     -analysis loc_loc
                        >
                        >
                        > Thoughts?  Or should I just not use
   selxavg3-sess?
                        >
                        > Katie
                        >
                        >
                        > ---------- Forwarded message ----------
                        > From: *Katie Bettencourt* <kcrum@bu.edu
   <mailto:kcrum@bu.edu>
              <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>
                     <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>
   <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>>
              <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>
   <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>
              <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>
   <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>>>
                        <mailto:kcrum@bu.edu
   <mailto:kcrum@bu.edu> <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>
              <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>
   <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>>
                     <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>
   <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>
              <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>
   <mailto:kcrum@bu.edu <mailto:kcrum@bu.edu>>>>>>
                        > Date: Tue, Nov 2, 2010 at 2:31 PM
                        > Subject: Questions about event related
              processing and
                        selxavg-sess and
                        > selxavg3-sess
                        > To: freesurfer maillist
              <freesurfer@nmr.mgh.harvard.edu
   <mailto:freesurfer@nmr.mgh.harvard.edu>
              <mailto:freesurfer@nmr.mgh.harvard.edu
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                        >
                        >
                        > Hi all,
                        >
                        > I've been trying to analyses both an event
              related and
                     block design
                        > experiments and have noticed a couple
   things
              that are
                     confusing
                        me and
                        > I would appreciate any help anyone
   could give me.
                        >
                        > 1.  In trying do the event-related
   analysis,
              I'm am a bit
                        confused by
                        > the FIR vs Gamma analysis and the use
   of the
              time window and
                        tprestim
                        > in the FIR analysis.  I have an experiment
              with 6 set size
                        conditions
                        > and 1 fixation condition.  each trial is 6s
              long with a
                     TR of 1.5
                        >
                        > I have run both of these commands:
                        >
                        >  mkanalysis-sess.new -analysis
   supIPS_loc -TR
              1.5 -paradigm
                        supIPS.dat
                        > -designtype event-related -funcstem fmc
   -motioncor
                     -runlistfile
                        > supIPSruns.txt -inorm -nskip 2
   -nconditions 6
              -gammafit
                     2.25 1.25
                        >
                        > mkanalysis-sess.new -analysis
   supIPS_loc -TR
              1.5 -paradigm
                        supIPS.dat
                        > -designtype event-related -funcstem fmc
   -motioncor
                     -runlistfile
                        > supIPSruns.txt -inorm -nskip 2
   -nconditions 6
              -tprestim 2
                        -timewindow 20
                        >
                        >
                        > The FIR gives me a time course window,
   which
              makes me
                     think that
                        > perhaps that is the one I want to use,
   but it
              shows very
                     little
                        > activation.  This data has been previously
              analyzed in Brain
                        Voyager,
                        > so I know it's not a case of the conditions
              not actually
                     causing
                        > activation, but for some reason, the FIR
              analysis doesn't
                     show any.
                        > I'm not sure if this is due to a bad time
              window/tprestim
                        settings, or
                        > something else.  However the gamma fit
              analysis shows a
                     bunch of
                        > activity where I expect to see it, but
   no time
              course window.
                        > (attached are pngs of the differences
   for the
              act_vs_fixation
                        > comparison).
                        >
                        >
                        > 2.  In addition, in both the event related
              (gamma) and a
                     normal
                        block
                        > design (different experiment) I get
   very different
                     results (at least
                        > for certain comparisons) depending on
   whether
              I use
                     selxavg-sess
                        (with
                        > stxgrinder-sess for each contrast) or
              selxavg3-sess.  The
                        differences
                        > are shown in the attached pngs
              (act_vs_fix-gamma.png
                     (which is the
                        > selxavg-sess and stxgrinder-sess
   analysis and
                        > act_vs_fix-gamma-selxavg3).  In the block
              design, both
                     selxavg3 and
                        > selxavg (+stxgrinder) give me very similar
              activation
                     when comparing
                        > two non-null conditions (ie.
   shape_vs_noise)
              but very
                     different (and
                        > similar to the differences in the attached
              pictures)
                     activations
                        when
                        > comparing against the null (ie
   shape_vs_fix or
              noise_vs_fix).
                         What am
                        > I doing wrong here?
                        >
                        > Thanks for your help!
                        >
                        > 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] selxavg-sess vs selxavg3-sess