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Hello freesurfer community,
I had asked this question before, however I am unable to reply to that thread. The question still remains unsolved.
I am trying to setup a retinotopy pipeline. I have analysed population receptive field data that generates polar angle and eccentricity maps which I project onto an inflated surface / flattened surface in freeview (Freesurfer 6).
MacOS 10.14.6 Freesurfer 6 Nipype (nipype version 1.5.0-rc1 (latest: 1.4.2)
I have two queries, which I think are connected.
1) Is there a way to display a circular/cyclic colour map (for the polar angle data) in the overlay screen? The existing 'color wheel' option seems linear(?) (i.e it doesn't not warp around).
2) The distribution of data overlayed changes/shifts compared to the RAW data distribution. I have linked the raw theta values generated from the pRF analysis (in radians) as a histogram and a polarmap - (the figures depict values for both hemispheres) and the distribution when I overlay it on the LH (the distribution for RH is similar)
See here for images: imgur[dot]com/a/Wo42DLd
This is my processing stream:
The raw theta values based on their voxel coordinates are affined to the
functional image and saved as a NIFTI volume. The NIFTI volume in functional space is transformed to the anatomical space and is converted to a surface using
! mri_vol2surf --src (input_file_theta.nii.gz) --o theta.mgh --hemi lh
--regheader sub-03/freesurfer/recon_all --projfrac 0.5
Any help will be appreciated :-)
--- From the old thread, there was this comment:
"*Hi!*
*Jumping in on this, since it has come up many times but is without a solution so far: the issue is that the color code is now mapped onto a straight color bar, not a circle. At the same time, it is not documented what color refers to which angle. That makes it very difficult to work with this kind of color bar. It would be very helpful to reintroduce the circle, and to explicitly document how angles are mapped to colors. Thank you! - Caspar (**Caspar M. Schwiedrzik)*
"
Thank you .
Cheers, Dev