We have been working on timecourse data that has had the prestim removed
(at the mkcontrast-sess level). The timecourses obtained with
roisummary-sess do not seem to correspond to the timecourses plotted with
tksurfer. The discrepancy is two-fold: the peak latency and the overall
timecourse shape. What could be the source of this discrepancy? This is
particularly obvious for the ALC (alcohol) and PLAC (placebo) conditions -
their peak activity is at the same timepoint in tksurfer but at different
points in the text output (as shown in the Excel file)
  Included are:
- The original text ouput file
- Excel file with the text output along with the graph,
- screen shots of the tksurfer timecourses and activity - on the left
side is the timecourse of the activity with prestim removed and on the
right is the timecourse with all the points
We have also included some of the relevant script
commands we used throughout the analysis.

The entire working directory can be found here...

/space/veles/3/users/sheeva/TEST-S51

This is the analysis I used...
analysis.info

analysis   SNfir-test
TR         2
designtype event-related
nconditions 4
parname    para.para
fsd        bold_SN
funcstem   fmcsm8
tpexclude

-timewindow 18
-prestim 4
-polyfit 2
-TER 2
-nskip 0
-fwhm 0
-extreg mcextreg
-nextreg 3

example of mkcont command...removing the prestim

entire script can be found
here.../space/veles/3/users/sheeva/TEST-S51/mkcont-sess.csh

setenv aa 1
setenv cc 0
echo '0 0 0 1 1 1 1 1 1' | mkcontrast-sess -analysis SNfir-test -contrast
CvFix-RMPS -a $aa -c $cc -rmprestim

stxgrinder-sess -analysis SNfir-test -contrast CvFix-RMPS -sf
51-SN-intragp

Finally, here is the csh that I used for making the timecourses....

setenv SUBJECTS_DIR /space/perun/3/users/cylix/Subjects

foreach roi (lh-AC-med)

foreach num (51)
foreach ltr (a j)

mri_label2label --srclabel
/space/veles/3/users/sheeva/fMRIanal/fsavg-labels/RMPS/surface/LH/${roi}.label
--srcsubject fsaverage --trgsubject sub${num}_recon --trglabel
sub${num}_recon/label/${roi}.label --hemi lh --regmethod surface

func2roi-sess -roidef ${roi}.label -labelfile
/space/veles/3/users/sheeva/fMRIanal/fsavg-labels/RMPS/surface/LH/${roi}.label
-d . -s sub${num}${ltr} -analysis SNfir-test

roisummary-sess -analysis SNfir-test -roidef ${roi}.label -d . -sf
SN51-a-j-RMPS -sumfile TEST-S51aj/Unmasked/LH/${roi}-unmasked.txt

end
end
end

Thank you
Elizabeth