Any publications related to colormap 'FreeSurferLabels' and algorithm of 'interpolate' checkbox?

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1

Hi,
I was wondering if any suggestion on finding publications related to colormap ‘FreeSurferLabels’?

Also I was wondering:

  1. what is the algorithm behind the checkbox (and toggle) ‘interpolate’ for displaying image (not the interpolate Resample Scalar Volume)?
    2 . And how is the interpolation resolution for the checkbox decided?

Thanks!

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2

Hi -

1 - freesurfer labels are from: https://surfer.nmr.mgh.harvard.edu/

2 - interpolation refers to trilinear interpolation when extracting a slice plane from the volume (for labelmaps interpolation leads to artifacts where the labels are mixed before lookup in the table)

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3

Thanks for your reply.
For question #1, I went to the webpage and didn’t find specific explanation of the description for this colormap ‘FreeSurferLabels’ used in slicer.

Thanks!

4

Can you provide more details about what you were looking for? The color table itself is just a mapping from numbers to colors - it only really makes sense if the numbers were generated by FreeSurfer.

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5

I am looking for the rational behind the number to color mapping.
I just found it this colormap worked well for my MRI images (not generated by free surfer).
Thus, I need some understanding and also justification of using this color map.

Thanks!

6

Maybe you can get some insight by reviewing the material and citations from the FreeSurfer wiki. The specific numbers and colors are an essentially arbitrary standard - maybe chosen to be easy to see by someone (maybe a neuroscientist who studied human vision?) who spent time picking, but as far as I know nothing more than that.

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