On Mon, Apr 11, 2011 at 12:22 PM, Douglas N Greve <
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu>> wrote:
You can run it anytime after the analysis. The 'X' file below is
an actual file that is there (X.mat). The value that you get out
of this procedure should be used to multiply the values you get
out of roisummary-sess.
doug
Katie Bettencourt wrote:
I'm working with Yaoda Xu. Thanks for the percent signal change fix, but I"m a little
confused by what you wrote. When do I run that? after running
roisummary-sess? Or after the analysis is run?
Also, is the load('X' a placeholder where I need to put
load('filename')? or will it just work as is? Obviously I
change the session and analysis in the cd line. And is that a flat scale factor for all conditions for that
subject?
Katie
On Fri, Apr 8, 2011 at 10:59 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>>> wrote:
btw, I notice that you have a harvard email now (was BU).
who are
you working with there?
doug
Katie Bettencourt wrote:
Hi all,
I'm doing ROI analysis on functional data with an
anatomical
label, and while the activity looks strong and robust in
tksurfer, the % signal changes I am getting are very
low (and
much lower than we've previously found), and I'm not sure
what's going on.
I'm running Freesurfer 4.5 on red hat linux.
The design is a blocked design with 4 non-null conditions,
baseline is fixation. Attached is a picture of the
activity I
get for 2 subjects for on of the conditions vs fixation
(baseline) at a p<0.05 threshold with the ROI outlined in
black as well as the output from roisummary-sess for
these two
subjects in that roi. I calculate % signal change based of
the output from roisummary-sess, dividing each condition by
the baseline in that file and then multiplying by 100. %
signal changes are listed below, along with all
commands run.
% signal change:
110222SKJ_connected 110222SP_connected
0.000988998467052 0.000533852720367
0.00105349836708 0.000556814127695
0.000408499366826 0.000327200054419
0.000440749316839 0.000436266739225
commands:
mkanalysis-sess -analysis connect -TR 2 -paradigm
connect.dat
-designtype blocked -funcstem fmc -motioncor -runlistfile
connect_runs.txt -inorm -tpexclude tpexclude.dat
-nconditions
4 -timewindow 20 -gammafit 2.25 1.25 -noautostimdur
mkcontrast-sess -analysis connect -contrast
connected_vs_unconnected -a 1 -c 2
mkcontrast-sess -analysis connect -contrast
connected_vs_noise
-a 1 -c 3
mkcontrast-sess -analysis connect -contrast
connected_vs_phase
-a 1 -c 4
mkcontrast-sess -analysis connect -contrast
connected_vs_fix
-a 1 -c 0
mkcontrast-sess -analysis connect -contrast
unconnected_vs_noise -a 2 -c 3
mkcontrast-sess -analysis connect -contrast
unconnected_vs_phase -a 2 -c 4
mkcontrast-sess -analysis connect -contrast
unconnected_vs_fix
-a 2 -c 0
mkcontrast-sess -analysis connect -contrast
noise_vs_phase -a
3 -c 4
mkcontrast-sess -analysis connect -contrast
noise_vs_fix -a 3 -c 0
mkcontrast-sess -analysis connect -contrast
shape_vs_noise -a
1 -a 2 -c 3
mkcontrast-sess -analysis connect -contrast
shape_vs_phase -a
2 -a 1 -c 4
mkcontrast-sess -analysis connect -contrast
shape_vs_noisephase -a 2 -a 1 -c 3 -c 4
mkcontrast-sess -analysis connect -contrast act_vs_fix
-a 2 -a
1 -a 3 -a 4 -c 0
selxavg3-sess -sf connect-sess -df connect.dir
-analysis connect
#run ROIs
setenv anal connect
foreach roi ( infIPS supIPS loc )
foreach h (lh rh)
func2roi-sess -roidef ${roi}-${anal}-${h} -analysis $anal
-anatlabel ips_loc/${roi}-${h} -sf connect-sess -df
connect.dir
roisummary-sess -sumfile ips-rois/${anal}_${roi}-${h}.dat
-roidef ${roi}-${anal}-${h} -analysis ${anal} -sf
connect-sess
-df connect.dir
python roi_reader.py -r ${roi} -a ${anal} -z ${h} -f
ips-rois -c 4
end
end
Thanks,
Katie
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
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