Problem on Atlas Reconstruction

Hi All,

I have used HCP atlas for individual atlas reconstruction. After labelconvert each participant’s left occipital part is kind of missing. Could you please help me with that?


Hi @cmid,

Is your diagnosis based entirely on the appearance of images such as that in the screenshot?

The purpose of labelconvert is typically to change the values stored in a parcellation image such that the parcels are valued from 1 to the number of nodes. That means that somewhere in the image, there are voxels within a parcel with the value 1. If the image is displayed using a grey colourmap, with the intensities corresponding to black and white determined based on the minimum & maximum values in the image, that means that the voxels within that parcel will be coloured just a shade brighter than black. So it’s possible that those parcels are not missing, they’re just extremely dark.

If you want convincing:

mrthreshold parcellation.mif -abs 0.5 - | mrview parcellation.mif -roi.load - -roi.opacity 0.2