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
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:
1. 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.
KatieOn 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:<kcrum@bu.edu <mailto:kcrum@bu.edu> <mailto:kcrum@bu.edu
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
<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
<mailto:freesurfer@nmr.mgh.harvard.edu>>
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<mailto:freesurfer@nmr.mgh.harvard.edu>>>>
> <mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
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<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>>
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<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
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<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>>>>>
>
>
> 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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<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>>>
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
-- 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
<mailto:greve@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
--
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
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html