I have only the polar angle condition, in two runs, one with positive and second with negative direction.

To process the data, I followed the steps listed here:

To my eyes, none of those images look like polar angle retinotopy maps.

I then visualized the angle.masked file (if I understand correctly, it is the angle map masked with p=0.01 significance), you can find the screen shot attached. It also doesn't look right, more importantly - it doesn't seem to be masked by significance. 

I have then followed the visualization instructions from the official FreeSurfer wiki, i.e: 

#!/bin/csh -f

set name = subject # put the subject’s name here

set hemi = lh

setenv eccendir eccen

setenv polardir polar

4

#setenv patch occip.patch.flat

setenv revpolarflag 1

setenv rgbname eccenthinmot

setenv fthresh 0.4

setenv fslope 1.3

setenv fmid 0.8

setenv angle_offset 0.77

setenv noexit

tksurfer -$name $hemi

I adjusted this script to my environment and run it on my machine. It doesn't work because it's missing the following input files:

sigf-lh.w

sig2-lh.w

sig3-lh.w

Indeed, those files do not exist in my folders. Does it mean that I made a mistake somewhere in the pipeline? Should those files be in my folders?

To sum up, these are my questions:
1) Do the enclosed maps seem alright to you? 
2) If not, do you have any idea at which processing stage there was an error? Or is it just a visualisation issue?
3) If this is a visualization error, how should I visualize the angle maps in freeview? Specifically, what output files should I use for this visualization? More specifically, what commands should I use to visualize these output files? For your information, these are my output files in the retino.lh/polar folder:

angle.masked.nii.gz  cesvar.nii.gz      fsig.nii.gz     mc.sig.dat
angle.nii.gz         cesvarpct.nii.gz   imag.nii.gz     minsig.nii.gz
cesmag.nii.gz        cwmap-imag.nii.gz  iminsig.nii.gz  real.nii.gz
cesmagpct.nii.gz     cwmap-real.nii.gz  mag.nii.gz      sig.nii.gz
ces.nii.gz           efficiency.dat     mc.ces.dat      z.nii.gz
cespct.nii.gz        F.nii.gz           mc.minsig.dat

4) what do the imag.nii and real.nii maps correspond to? I believe they represent the real and imaginary component of the Fourier transform, but how do I interpret it in terms of retinotopy results?

I would be very grateful for any help.

Take care, Kasia