This page describes how to run the retinotopy analysis of the FreeSurfer Functional Analysis Stream (FS-FAST) version 5.X. You will need to know how to run FS-FAST for genernal task related studies. See for more info.

1. Create Paradigm Files

For each session, create retinotopy paradigm files in each of the run directories:


.../session/bold/002/rtopy.par (etc.)

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 angle stimulus and in what direction the stimulus was presented. THESE ARE SIMPLE TEXT FILES! DO NOT CREATE THEM WITH MS WORD!

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 is positive and what is 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:

stimtype eccen

direction neg

The polar type in the positive direction would look like this:

stimtype polar

direction pos

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

2. Run preprocessing

preproc-sess -surface self lhrh -fwhm 5

3. Create the analysis

In the example below there is a 30 second period, and 'rtopy.par' is the name of the paradign file from above.


-a rtopy.self.?h \

-surface self ?h \

-TR 2 \

-retinotopy 30 \

-paradigm rtopy.par \

4. Run the analysis:

selxavg3-sess -a rtopy.self.?h -sf ...

5. Create the field sign map:

fieldsign-sess -a rtopy.self.?h -occip -sf ...

This command assumes that you have created an occipital patch. If you have not, either do so (see FreeSurferOccipitalFlattenedPatch) or run with -sphere instead of -occip.

6. View individual results

a. Significance maps:

tksurfer-sess -a rtopy.self.?h -s sessid

b. Display raw angle:

tksurfer-sess -a rtopy.self.?h -s sessid -map angle

c. Display angle masked by sig:

tksurfer-sess -a rtopy.self.?h -s sessid -map angle.masked

d. Display field sign:

tksurfer-sess -a rtopy.self.?h -s sessid -fieldsign

FsFastIndividualRetinotopyAnalysis (last edited 2011-02-23 12:00:04 by tanha)