Hello,
I am trying to calculate the percent signal changes for my monkey data.
I did this by running the command selxavg3-sess and looking at the cespct
values (or equivalently by using h.nii divided by h-offset.nii).
I found in the mailing list that this value should be corrected by a scaling
factor scalef if freesurfer-4.5.0 is used (see below).
If I apply this correction factor I got values that at first sight look
reasonable but if i calcultate the psc using JIP (the imaging program from Joe
Mandeville), i find different values.
And looking at the raw data I have to conclude that the value from JIP are the
correct ones...
For example if i look at the same voxel in MT if find:
with JIP: -14.45%
with FS: -8.15 %
notice that the values are negative and pretty large due to the fact that we
use and iron oxide contrast agent.
If, instead of applying the scaling factor scalef (defined below), I apply the
factor max(x.X(:,1)) as a scaling factor (which according to me is the maximum
value of the convolved design matrix,or 'the EV' in FSL lingo),
then I end up with a value of -15.09%. Which is pretty close to the value
obtained with JIP.
I got the last idea from mumford.fmripower.org/perchange_guide.pdf
Do you have any clue where the differences come from? or if I am doing
something wrong?
Also, one of my colleagues used both the gamma model and FIR model to calculate
the percent signal change (psc) for his event-related designed experiment, and
the values are also quite different.
He applied the scaling factor for the values from the gamma model, and didn't
do it for the fir model. What he got is 0.6% signal change if he takes the peak
of the time course (which looks quite ok) that fitted from the FIR model
and 1.5% signal change from the gamma model. It seems that there is more than 2
times differences between these two values. Is it normal, or we need another
scale factor for the fir model?
Thanks for the answers!
regards,
Thomas Janssens
ps:
My selxavg3-sess analysis was done using the following parameters in the
analysis.cfg file:
-gammafit 0 8
-gammaexp 0.3
-timewindow 40.00000000000000000000
-prestim 0
-acfbins 10
-fix-acf
-autostimdur
-no-fsv3-st2fir
-no-fsv3-whiten
-polyfit 2
-TER .10000000000000000000
-autowhiten 30
-nskip 0
-fwhm 0
-rescale 1000
----------------------------------------------------------------------------------------------
>[Freesurfer] Calculating % Signal Change from roisummary-sess readout
>
>Douglas N Greve
>Wed, 04 Aug 2010 14:25:52 -0700
>
>
>That's right, though you may/will run into the problem of very small
>values in which case you can use this fix:
>
>cd bold/analysis
>x = load('X');
>tirf = x.flac0.ev(3).tirf;
>Xirf = x.flac0.ev(3).Xirf;
>scalef = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)]));
>
>scalef will be something like 184. Multiply the percent signal change
>you get by this number. BTW, this problem is fixed in version 5.
>
>doug
>
>
>Adam Nitenson wrote:
> Hi Freesurfers,
>
> I am trying to analyze functional activity in individual subjects.
> The structural constraint is a dACC label and the functional
> constraint is positive activation at a specific timepoint (6 sec
> after stimulus). I was just wondering what the numbers following the
> "# of estimates per condition" row actually represented, and how I
> could convert these to % signal change. I saw in an archived email
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00171.html
> that someone mentioned taking those values, dividing by the baseline
> offset value (row 4) and multiplying by 100 to get % signal change.
> Is this a valid method?
>
>
> Adam Nitenson, B.S.
> Brain Genomics Lab
> Massachusetts General Hospital
----------------------------------------------------------------------------------------------
Thomas Janssens, PhD student
Laboratorium voor Neuro- en Psychofysiologie
K.U.Leuven Medical School
Herestraat 49, B-3000 Leuven (Belgium)
phone +32 16 33 00 35
cell phone +32 494 115 509
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