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Sorry, this is the actual link to the images: https://drive.google.com/open?id=1SLPgXmPiqHCyKLHcxKYonyHBl_3pdFzS

Marco

On Thu, 6 Feb 2020 at 14:44, Marco Ninghetto m.ninghetto@nencki.edu.pl wrote:

Dear FREESURFERs, I'm performing retinotopy analysis. I preprocessed data and made 1st level analysis. Stimuli definition is: 6 cycles of rotating wedge (counter-clockwise rotation) and 6 cycles of expanding ring. One cycle lasts ~41 seconds. Scan TR = 2.5 sec.

I followed the pipeline below (after recon-all):

preproc-sess -sf sessid -fsd bold -fwhm 5 -surface self lhrh -per-run

mkanalysis-sess -a ret_?h -surface self ?h -fwhm 5 -retinotopy 41

...

-paradigm rtopy.par -TR 2.5 -fsd bold -per-run

selxavg3-sess -a ret_?h -s SUBJ01 (let's say first subject)

I created an occipital flat patch and then:

fieldsign-sess -a ret_?l -patch lh.occip.patch.flat -s SUBJ01

...

Then, I visualize results using

tksurfer-sess -a ret_?h -s SUBJ01 -map angle -tksurfer

tksurfer-sess -a ret_?h -s SUBJ01 -map angle.masked -tksurfer

tksurfer-sess -a ret_?h -s SUBJ01 -tksurfer

tksurfer-sess -a ret_?h -s SUBJ01 -fieldsign -tksurfer

I'm not sure about the activations I get and I'm not sure how to interpret these data. What are the colors in the colorbar telling me? What is fieldsign img showing? what's the difference between raw angle and angle.masked (is this the mask created during preprocessing?)? In angle.masked result, the red part is the center of population receptive fields deducted from eccentricity or from polar?

Here the link to the folder with images https://drive.google.com/open?id=1ers6Cq9uYEEZnCUHZyFlqtzevV7d-xyg

Any help on interpreting these results would be much appreciated. Thank you, Marco

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Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland