Hi Thomas, you may have found a bug in my scale factor calculation. Can
you compute the new scale factor as described below? BTW, these issues
are fixed in version 5.
cd bold/analysis
x = load('X');
tirf = x.flac0.ev(3).tirf;
Xirf = x.flac0.ev(3).Xirf;
scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)]));
TR = x.flac0.TR;
dt = tirf(2)-tirf(1);
scalefNew = sum(Xirf)*TR/dt;
Thomas Janssens wrote:
> 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
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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