help > Unable to select colors for Atlas-defined ROI overlay
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Dec 2, 2020  07:12 PM | Rigina Gallaghr
Unable to select colors for Atlas-defined ROI overlay
Hello, 

I am new to using MRIcroGL so the following is probably a very basic question/problem. I am using MRIcroGL provided MNI brain image as a template and overlaying AAL-atlas-defined ROIs over that template image.. I am loading in the AAL-atlas ROIs from my own computer files. When I load in the ROIs that I would like to display on the MNI template brain image, the "color" option is greyed out, so I cannot select the color for any ROI. This is not the case when I load in JHU-defined ROIs from my own files (I can select the color for each ROI that I overlay just fine).

Any advice would be appreciated.


Kind regards,
Rigina
Dec 2, 2020  08:12 PM | Chris Rorden
RE: Unable to select colors for Atlas-defined ROI overlay
1. I am going to assume you have a uncompressed NIfTI image (e.g. img.nii), if you have a compressed image ("img.nii.gz") uncompress it first.
2. Open the image with MRIcroGL
3. From the "Layers" panel, choose the Options->ShowHeader button
4. Select the "Statistics" tab, set the "Intention" pull down menu to be "Labels"
5. Choose the File/SaveHeader menu item and overwrite the header of your image.
6. Reopen your image, it is now recognized as a atlas with discrete regions, not a scalar image.
Dec 18, 2020  02:12 PM | Rigina Gallaghr
RE: Unable to select colors for Atlas-defined ROI overlay
Thank your so much for your advice! I did follow it but am still having the same issue. I also made sure my .nii files were uncompressed. When I loaded in the overwritten image as an Overlay, the "color" area was still greyed out and pre-selected to something random (like CT-Kidney). 

To be clear, I am loading in individual ROIs as overlays one at a time; not loading in an entire atlas at once. Would that make a difference?


Thank you, 
Rigina
Dec 18, 2020  02:12 PM | Rigina Gallaghr
RE: Unable to select colors for Atlas-defined ROI overlay
I was able to fix the issue. I followed the advice given above and selected the statistic to be set to "not statistics" rather than to "labels". For some reason this worked. Thank you!

Best, 
Rigina