Hi again,

I noticed that this problem occurred only in freeview. The annotations are correctly displayed on tksurfer: the labels are shown in the expected colors and the alpha channel works fine. The surface remains visible outside the labels and is not black.

My freeview version was 1.0 My FreeSurfer version is v5.3.0 Mac OS X 10.10.5 (Yosemite)

Sorry for (kind of) spamming!

Have a nice weekend, Michael

On 11/03/16 17:04, Michael Bannert wrote:

Dear Freesurfer community,

I have a problem using the alpha channel in the color lookup tables. No matter what values I choose, none of them seem to affect the transparency in any way.

Here is what I would like to do: I have a number of labels that I want to visualize on an inflated brain surface of fsaverage (with a binarized curvature map). So I use mris_label2annot to create an annotations file which I later load in freeview.

mris_label2annot \ --s fsaverage \ --h rh \ --annot-path path/to/rh.output.annot \ --ctab /Applications/freesurfer/SegmentNoLUT.txt \ --l path/to/first.label \ --l path/to/second.label

When I load this file into freeview, I can see the two labels without a problem. However, everything outside the labels is just black. I assume that's because all vertices that don't fall into any of the labels, are assigned the first RGBA value, which is [0 0 0 0] by default.

Now, I would of course like to see the rest of the brain surface. I figured I could do that by changing the alpha channel of the Seg0 entry in the color lookup table. But no luck: everything outside the labels appears black.

I also don't understand the function of the --no-unknown argument. I was under the impression that this would make sure that vertices that are not part of any label would not be assigned any color and therefore... well, appear transparent? (which whould be good) ... appear black? (which would be bad)

Any ideas?

Thanks & best, Michael _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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