It is feasible to use ROIs crated with Jim (Xinapse) in another program (MRIcron)?

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Francesco Patti

I apologize

I do not have the expertise to address this question

Loredana Storelli

I don't think it is possible because they are saved as text files but I don't think they are in a format compatible with other programs. But I never tried it, so I'm not sure about this.

Mark Horsfield

Jim uses geometric shapes to define the regions, while MRIcron labels a set of voxels. In MRIcron, a voxel is either inside or outside a ROI, while in Jim, a voxel may be partly in or partly outside a ROI. Therefore the two types of ROI definition are incompatble.

If you want to get ROIs created with Jim into MRIcro, you need to convert Jim's type of ROI into voxel labels. This can be done using the 'Masker' tool. It takes Jim's ROIs and a uses them to mask an input image, creating an output image where all voxels outside the mask are set to a background value of zero.