Retinotopy analysis in FS-FAST


For each session, create retinotopy paradigm files in each of the run
directories.  These paradigm files are different than an event-related
or block paradigm (which list which stimulus was presented when).  A
retinotopy paradigm file has information about whether the run was an
eccentricity or polar stimulus and in what direction the stimulus was
presented.

For polar, the direction is indicates whether the spoke was traveling
clockwise or counter-clockwise.  For eccen, the direction is indicates
whether the ring was expanding or contracting.  The definition of
what's positive and what's negative is arbitrary, though it must be
consistent.  If you don't have both directions, just use positive.

For example, if there were four runs (001, 002, 003, 004), two eccen
and two polar, both in the positive and negative directions.  Create a
file (eg, rtopy.par) in each run.  Assuming run 001 was eccen in the
negative direction, then the rtopy.par for run 001 would look like:

--------cut here --------
stimtype  eccen
direction neg
--------cut here --------

If needed, create a run-list file with the all retinotopy runs
(regardless of whether it was eccen or polar).

Create the analysis:

mkanalysis-sess \
 -a rtopy   \
 -TR 2   \
 -designtype retinotopy  \
 -paradigm rtopy.par  \
 -funcstem fmcsm5  \
 -ncycles 8


Preprocess
  preproc-sess -s avdk -fwhm 8

Run the analysis:
  sfa-sess -s avdk -a rtopy

This will create avdk/bold/rtopy in which will be:
  1. volume h-offset (the mean function intensity)
  2. eccen - eccentricity folder (with h volume)
  3. polar - polar folder (with h volume)

The task-related activation can be viewed as with any other contrast
in a non-retinotopy application.  Just use eccen or polar as the
contrast and specify h as the map.

The task-related activation for eccen can be viewed with:
  sliceview-sess -s avdk -a rtopy -c eccen -map h -slice mos
The task-related activation for polar can be viewed with:
  sliceview-sess -s avdk -a rtopy -c polar -map h -slice mos

Run paint:

  paint-sess -a rtopy -s avdk

This will create map-imag-lh.w (the imaginary or sine part multiplied
by the log10(sig)), map-real-lh.w (the real or cosine part multiplied
by the log10(sig)), and sig-0-lh.w (the task related activation) for
both the polar and eccen.  It will also create a directory called
fieldsign in bold/rtopy in which fieldsign-lh (or -rh) along with
fieldsignmask-lh will be found.

To view the field-sign on the flattened patch (occip.patch.flat):
  surf-sess -s avdk  -a rtopy -retinotopy fieldsign -flat

To view the eccen on the flattened patch (occip.patch.flat):
  surf-sess -s avdk  -a rtopy -retinotopy eccen -flat

To view the polar on the flattened patch (occip.patch.flat):
  surf-sess -s avdk  -a rtopy -retinotopy polar -flat

To view the task-related polar activation on the flattened patch
  surf-sess -s avdk  -a rtopy -c polar -flat