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
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