Hi FSL community,
I’ve been reading this forum for a while now and have found this information quite useful as I’ve been working with neuroimaging data first at University of Wisconsin-Madison, and currently at University of California, San Francisco. I’m now posting my first question, which I am hoping will be a simple one:
What command line tools would I use to fill in the outline of a mask? I have 3D anatomical nifti images with ROI masks, but they came from GE BrainWave software which presents them as outlines and I need to fill them in to be proper masks. Something that implements a flood fill algorithm?
More detail:
I have a structural 3D nifti scan, with the anatomical brain ranging from intensity values of
0-350, and outlines of ROIs drawn in intensity value of 32767. I need to convert these to proper ROI mask images.
I was able to convert the image into a mask with values of 0 and 32767 using -thr in fslmaths. But I can’t figure out how to fill in the outlines without using interactive display tools.
Thanks!
Maria
|