help > MRIcroGL doesn't show tmap when thresholded
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Oct 5, 2020  09:10 AM | ricarda schubotz
MRIcroGL doesn't show tmap when thresholded
Hi there and sorry for silly problem postings but ... we faced the problem that MRIcroGL does not display any voxels of a tmap when it was thresholded beforehand. for instance when trying to visualize a conjunction which contains lots of zero voxel values and only some blobs with above zero voxels. can anybody help, please? many thanks in advance!
Oct 7, 2020  12:10 PM | Chris Rorden
RE: MRIcroGL doesn't show tmap when thresholded
I believe this is a duplicate of https://github.com/rordenlab/MRIcroGL12/issues/17
Oct 7, 2020  01:10 PM | ricarda schubotz
RE: MRIcroGL doesn't show tmap when thresholded
Hi Chris

Thanks so much for your quick reply and for pointing to this issue "Interpolating Thresholded Images #17" but unfortunately that did not solve my problem. I attach a screenshot showing the same overlay in MRIcroGM (where the activity spot is gone) and MRIcron (where it is displayed). overlay loading is NOT smoothed, as can be seen in the screenshot. hope I did not miss any important point ...

many thanks for further ideas
Ricarda
Oct 7, 2020  04:10 PM | Chris Rorden
RE: MRIcroGL doesn't show tmap when thresholded
Thanks for sharing an example of the dataset. This is a duplicate of 
  https://github.com/rordenlab/MRIcroGL12/issues/17
Sub-threshold voxels have been artificially set to "Not-A-Number" values, and then the image  is being interpolated onto a higher resolution image. You will always get a better result if you reslice PRIOR to thresholding. The thresholding is eliminating crucial information. The current pre-release of MRIcroGL tries to explicitly identify not-a-number data to. mitigate the consequences. However,  throwing away a lot of information prior to interpolation will always incur some penalty.