Dear Michael,

You've pretty much got it.
The list of points 1-5 are all correct except for:
 - units are in seconds, not milliseconds
 - T2* changes are all relative to the baseline, static value
and not the prior volume (as 1 seems to imply, but
conflicts with what you say in 2, which is correct)

So you need to scale the values in your 4D file to represent
changes in T2* in units of seconds (e.g. 0.001 would represent
1 millisecond).

S0 is an intensity value not a T2* value, so it is in arbitrary units
and not in seconds or milliseconds. The S = S0*exp(-TE/T2*)
equation is about _intensity_ values. So if you had a TE of 30ms
and a T2* of 51ms then S=S0*exp(-30/51) = 0.55531*S0
whereas if T2* increased by 5.1ms (an increase is what you'd
expect with more activation, as there's less deoxyHb and less
field distortion, so longer T2*) then you'd have an intensity of
S=S0*(-30/56.5) = 0.58803*S0. This would represent a
signal increase of 0.58803/0.55531 = 1.0589 (or about 6%).
Note that this signal increase is more simply calculated as
exp(-TE/T2*B +TE/T2*1) where T2*A and T2*B are the two relevant
T2* values (so exp(-30/56.5 +30/51)=1.0589).

Therefore, to achieve a certain value of percent signal change
(which is normally what people think about) then you need to
solve the equation: exp(-TE/T2*B + TE/T2*A)=desired factor
setting T2*A=51ms and TE and desired factor as appropriate.
For example, a 10% signal change, with a 30ms TE, means:
  exp(-30/T2* + 30/51)=1.1 => -30/T2* + 30/51=ln(1.1)
 => T2* = 30/(30/51-ln(1.1)) = 60.8 and so the change in T2*
that would need to be encoded in the 4D activation file would
be 60.8 - 51 = 9.8ms = 0.0098 seconds.

I hope this helps explain how this part works.

You do need to specify the --activt4D input.

You can limit the voxels that POSSUM calculates by changing
the input brain object. It will only calculate things for object
voxels present in this image. So feel free to take the default
brain and mask out whatever you like. This will certainly speed
things up, although it won't give you the right solutions in the
case of motions, as you need the other voxels present, but I
don't know if that is of interest to you or not.

All the best,
Mark




On 24 Jan 2012, at 19:37, Michael Hallquist wrote:

> Dear FSL gurus (especially Mark and Ivana):
>
> I have a question about how to setup a 4d activation timecourse file
> using simulated time series not generated from empirical fMRI data. I
> realize that there have been a number of questions on the listserv
> about how to specify these files and I've read through these posts in
> detail. Yet I'm getting stuck on how to properly scale time series
> that are in arbitrary units and where there is no task baseline per se
> (resting state data).
>
> Here's the summary of what I've understood (and please let me know if
> I've misunderstood!):
> 1) The 4d activation file provides voxelwise timecourse specifications
> of T2* changes (i.e., units are T2star dt [delta time], relative to
> prior volume).
> 2) The time course units are milliseconds (representing relaxation
> time) and are relative to the baseline T2* relaxation value specified
> in the MR parameters file. In the case of the stock MRpar_3T file, the
> T2* relaxation time for gray matter is 51ms.
> 3) A value of 0 at any point along a voxel timecourse in the 4d
> activation file means that the intensity will be based on the static
> T2* value alone (51ms per above).
> 4) T2* values are related to simulated signal intensity by the
> following equation: S = S0 * exp(-TE/T2*), where S0 is the baseline
> intensity, TE is the echo time, and T2* is the absolute T2* value.
> 5) To generate signal intensity at a given voxel and timepoint, POSSUM
> sums the T2* value of the static tissue type (51ms above) plus the
> voxelwise, time-specific value in the 4d activation file (e.g., 5.1).
>
> Now to my questions. I have simulated correlated time series in
> arbitrary units that are scaled roughly [-2, 2]. How do I scale these
> time series into the appropriate T2* units for the --activ4D input
> given the equation above? In my case, is S0 51ms or do I need some
> baseline intensity in arbitrary scanner units?
>
> Also, If the static T2* time for gray matter is 51ms and I provide a
> value of 5.1 at the given point in the timecourse, does that
> correspond to a 10% signal change?
>
> Do I always need to specify --activt4D to provide the times for the 4d
> activation file, or will these be computed based on the TR encoded in
> the NIfTI of the activation file?
>
> Lastly and most peripherally, I realize that the 4d activation results
> in computationally and RAM-intensive simulations, which is fine. Is
> there a way to reduce the RAM or computation burden using a mask file
> (simulation within a sparse matrix of sorts)?
>
> Thanks very much for your help,
> Michael
>