Hi Doug,
I am running into a similar problem that Yuko describes in Martinos Tech
message 5099 (wouldn't let me reply directly). Using Stable 4, I made an old
analysis last spring and extracted ROI values, yielding significant differences
between two conditions as expected. I believe I originally used
mkanalysis-sess.new. I later redid some func2roi analyses after redoing
mkanalysis-sess (rather than .new) and the significant difference was gone even
though the data set and label were the same, so I tried to recreate the same
old analysis with the .new added back in. However, I noticed that my
roisummary-sess outputs are still different:
*Original -->
ID100 104 104 395.4163 31.5163 258.00 3.000 -0.00 7 1 -0.1397 0.6388 3.3232
3.9929 -18.0485 -6.8824 -7.0568
mkanalysis-sess -inorm (autosets -TER to 0.15) = mkanalysis-sess (no -inorm)
(autosets -TER to 0.15) -->
ID100 104 104 431.8531 31.1137 258.00 0.150 -0.00 7 1 -1.6920 -1.7342 -1.6874
-2.2781 -1.9065 -1.6461 -2.1075
*mkanalysis-sess.new -TER 3.000 -inorm = mkanalysis-sess -TER 3.000 -inorm =
mkanalysis-sess -TER 3.000 (no -inorm) -->
ID100 104 104 431.296 31.1078 258.00 3.000 -0.00 7 1 -33.3915 -34.3076 -33.5928
-44.2051 -37.5009 -31.9037 -41.6321
mkanalysis-sess.new -TER 3.000 (no -inorm) -->
ID100 104 104 233.0353 16.8080 258.00 3.000 -0.00 7 1 -18.0419 -18.5369
-23.8846 -20.2622 -17.2380 -22.4944
The two * analyses should be identical (all the same settings during
mkanalysis-sess.new), but for some reason aren't.
Besides there being a large range among the values (-0.1397, -1.6920, -18.0419,
-33.3915), in the previous extraction there were some positive values, whereas
now there are mostly negative values. I noticed that the TER column was
different between the original and the new one (both were originally
nonspecified and used the autoset -TER of 3 for the original and 0.15 for the
new), so I tried making a new analysis specifying TER as 3.000 in both
mkanalysis-sess and mkanalysis-sess.new, as well as turning -inorm and
-autostimdur on and off.
When using mkanalysis-sess I primarily get large negative values (-33.3915
-34.3076) and -inorm, -autostimdur, & -noautostimdur don't make much of a
difference if any. If I change the -TER (3.000 0.0300 0.150) my values change,
with larger negative values with 3.000 and smaller values with 0.0300. However,
even with setting the TER to 3.000 as in the original analysis, my values do
not come out the same as we originally found.
I was wondering, what is the difference between the mkanalysis-sess and
mkanalysis-sess.new commands and why do they result in such different func2roi
values? The volumetric maps look identical for all of the analyses, so the
problem seems specific to the ROI signal extraction. Also, how do you decide
what TER to use? Our TR = 3.000 s, TE = 0.0300 s, and the paradigm files were
set up in intervals of 3.000 s. I'm not sure if the scan parameters' TE value
is the same as the mkanalysis-sess TER setting.
We would like to compare ROI % signal change extracted from the same ROI from
two different phases (day 1, day 2). However, if we use the original ROI
extraction values, we get % Sig Ch values in the -0.3 to 0.3 range, whereas
with the new ROI extraction values, we get % Sig Ch in the -0.008 to 0.01
range, and the scale of the values seem incomparable. Any idea what might be
going on or how to get something more like the original values?
Thanks,
Garth
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