Hello Everyone,
I am a new FreeSurfer user, trying to do retinotopy. My stimulus has the following configurations:
- 96 TRs in total per run, including 8 blanks in the beginning and 8 in the end - Polar angle: - bowtie checkerboard wedges - 16 unique positions - 5 repetitions per run - 2 TRs per position per run = 80 stimulus TRs per run. - counterclockwise or clockwise rotation
- Eccentricity - checkerboard annuli - 16 unique eccentricities - 5 repetitions per run - 2 TRs per position per run = 80 stimulus TRs per run - expanding on contracting
I have 3 runs of CCW wedges, 3 runs of CW wedges, 2 runs of expanding annuli and 2 runs of contracting annuli.
I have used this guide by Xu Cui as a template for directory structure and analysis: http://www.alivelearn.net/?p=65 I
I have made appropriate .par-files and placed them in the folder for every run. In mk-analysis-sess.new I set ncycles to 5 (because I have 5 repetitions per run). After I paint the results on the flattened map the eccentricity map looks like other maps I've seen, but this the polar map looks awful - like random spray paint on the flattened surfaces, and with a lot of space with no coloring, even close to the calcarine. The field sign maps are completely empty, not even the flattened surface shows up (I don't know how they are supposed to look, but its all black).
I have tried several solutions: a) removing the blank TRs from my functional data files, so that only stimulus TRs are included in my analysis. b) setting ncycles to 10 (because we essentially have two polar wedges on the screen at each position). But none of this has helped. I am also somewhat unclear on the settings inside surf-sess. For example, what do I set the values in phase encoded data display at?
I would be grateful for any suggestions that might help - if you need to know anything else about my stimulus or analysis, please let me know.
Best,
Peter K.