hi gregory,

to address your last question: no, tksurfer does not require both eccentricity and polar angle data to display either coordinate map by itself. as bruce wrote, the convention is that the eccentricity and polar angle data are each stored in two separate overlay or ".w" files. the ".w" files each contain a list of (real-valued) floats corresponding to the real and imaginary parts of the complex-valued temporal FFT. these two files are reassembled by tksurfer, which can then display the phase with a cyclic color wheel for each visual field coordinate independently.

briefly, after you generate the pair of ".w" files for, say, the polar angle coordinate with 'mri_vol2surf', you can load the overlays into tksurfer for visualization. just load the overlay for the real part then the overlay for the imaginary part with 'File -> Load Overlay', which will load each into a separate overlay layer. (since your data is in structural space you won't have to specify any registration when you load in those overlays.)

to view the phase of the complex-valued data, open the 'View -> Configure... -> Overlay...' window and select the complex color wheel as the Color Scale, and select the "Complex" display option. depending on how your data is scaled, you may want to adjust the display thresholds.

of course to compute (and subsequently display) the "field sign" overlay, you will, however, need overlay files for both eccentricity and polar angle.

hope that helps!

-jon

On Fri, 30 Jun 2006, Doug Greve wrote:

What is the nature of the complex data? Ie, what format is it in? mri_vol2surf will convert shorts, ints, and floats, single and multiple frames/timepoints, but it will not specifically handle complex. I was not aware that any format could code complex, but maybe nifti can?

doug

Bruce Fischl wrote:

...

Hi Gregory,

I'l leave the mri_vol2surf to Doug, but basically we treat the components separately - one file for the real and one for the imaginary. You should convert each of them to a .w file. You can display either with a color wheel in tksurfer. Jon Polimeni is the current expert on this stuff, so I'll cc him.

cheers, Bruce

On Fri, 30 Jun 2006, Gregory Scott wrote:

...

We have complex-valued volumes (retinotopic mapping data) in structural space (1,1,1mm)

We'd like to convert this to a surface overlay (.w)

Can mri_vol2surf handle complex data and can Freesurfer display this? (with some sort of color wheel scheme)

Also, does freesurfer require both polar and eccentricity mapping data simulateously or can one display (eg. polar mapping) data separately?

Thank you very much for your time and any help Sincerely, Gregory Scott _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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