Hello Everyone
I am working with a paediatric data set, particularly interested in the basal ganglia. I’ve found FIRST does a poor job of parcellating the subcortical structures for these scans, but I’ve been very happy with the results from MAPER. I’d like to edit the 5ttgen output to replace the sgm volume with the result from MAPER (extracting the relevant parcellations from this and combining to create a binary mask). Feeding this into 5ttedit with the -sgm option then labels the voxels supplied in this mask as sgm, which appears to add to the SGM volume in the 5ttgen output, and subtract these voxels from the other tissue files (gm, wm etc). This works nicely, but there are voxels labelled as the sgm originally, which I’d like to remove, and allocate to generally white matter. Is there an easy way to do that?