Help RetinoProc stimulus

AFNI Message Board
1

Hello Afni experts
I am trying to use RetinoProc for a retinotopy analysis and I have a doubt about it. In the various scripts in the demo I see that there is no input field in which to enter the initial phase of my visual stimulus (be it the wedge for polar angles or the ring for eccentricity). Should I assume that whatever the initial phase of the stimulus is, the result is not affected, or does Afni take a default value (such as zero degrees for the wedge) as the initial phase?
Thanks in advance for your answer!!!

Luca

2

There doesn’t appear to be an option to set the initial phase, and zero degrees is assumed. You should see this in the output files. You can modify the output as you like by adding or subtracting from the niml.dset output.

3

I really thank you for the answer
If possible I would have another question.
By running the RetinoProcDemo script, in the eccentricity map obtained through @Proc.All I have that the apex of the occipital lobe is activated for higher degrees of eccentricity and then the trend goes decreasing going toward the center of the brain (pic1). In one article, however, I saw that the output of SUMA is the opposite (pic2). And this happens in many other papers. Why this difference?

Luca

pic1.png

pic2.png

4

I’ve never looked at this demo nor this data, and I’m no expert on retinotopy, so I’m hoping we can figure some of this out together. I don’t see the same image that you show. The retinotopy results include both phase and power columns for the surface data. If I show phase and threshold by the power, I get something fairly close to the second image. (See attached) Except for the occipital pole, the phase generally decreases in the demo data as it moves anteriorly within the posterior cortex. The settings used here for the display set the Sym off, min=0, max=360, and I’ve used the same color scale. To get this to run properly, I had to do this :

@AfniEnv -get AFNI_1D_ZERO_TEXT
@RetinoProc -install_demo
(if there are problems, then cd AfniRetinoDemo ; tcsh -x ./@Proc.All )

Start Demo display with :
cd RetProcOut.All
tcsh @ShowResult

The @Proc.All script calls @RetinoProc this way:

@RetinoProc
-sid Hildebrand
-surf_vol SUMA/Hildebrand_SurfVol+orig.HEAD
-spec_left SUMA/Hildebrand_lh.spec
-spec_right SUMA/Hildebrand_rh.spec
-anat_vol afni/Hildebrand_3_1.nii
-TR 2
-period_ecc 32
-period_pol 32
-nrings 1
-nwedges 2
-fwhm_ecc 8
-fwhm_pol 8
-pre_ecc 16
-pre_pol 16
-ccw afni/Hildebrand_4_1.nii
afni/Hildebrand_8_1.nii
afni/Hildebrand_12_1.nii
-clw afni/Hildebrand_5_1.nii
afni/Hildebrand_9_1.nii
afni/Hildebrand_13_1.nii
-exp afni/Hildebrand_6_1.nii
afni/Hildebrand_10_1.nii
afni/Hildebrand_14_1.nii
-con afni/Hildebrand_7_1.nii
afni/Hildebrand_11_1.nii
afni/Hildebrand_15_1.nii
-out_dir RetProcOut.All
-no_tshift

retinoprocdemo.png
retinoprocdemo.png1212×605 171 KB

5

Thank you very much for the prompt response.
I ran the script exactly as you enunciated, the difference between mine and your image I believe is simply because I mapped the Hildebrand.sm.lh.ecc.niml.dset file while you mapped the Hildebrand.sm.lh.ecc+.niml.dset file
The doubt was really about the fact that in this demo, as you also noted, the phase decreases starting from the lobe and going toward the inside of the cortex, while in various papers the opposite is shown. I am probably mistaken in something and was wondering where.

Luca