dHCP Preprocessing runs successfully but creates a partial sphere

The dHCP minimal preprocessing runs successfully, however, several subjects have a strange partial sphere.

I was wondering if anyone else has encountered such an issue?

Hi Adebayo

Have you checked the other meshes - e.g. white? What about the volumes and volumetric segmentation files? It will be useful to track back through the pipeline to figure out where it first goes wrong.



Hi Emma,

Thanks for responding.

Looking at the other meshes, nothing appears to be different from any of the other meshes that underwent surface reconstruction without any problems. Additionally, the volumes and volumetric segmentations appear to be be good as well.


Can you send the surface and white matter and T2w_restore.nii.gz files please?

Sure thing.

Does a link to a google drive work?: https://drive.google.com/file/d/1Fj7AiUV_0yu_PdckinhdsvTBpLLZFKu5/view?usp=sharing

Thanks - inflated also, please!

Sure thing, my apologies: https://drive.google.com/file/d/19E44meLVIm3Bne5-3nfBZ7CnX0wrUf8x/view?usp=sharing

So we ran mesh-to-sphere (spherical projection) again on it’s own and it worked fine. We don’t really know why it went wrong for you but you can try re-running with -debug. This saves a number of intermediate meshes at each level (e.g. before/after SMDS, before/after postprocessing etc) so you can see where the failure occurs. Here is your sphere as a vtk file


Thanks Emma.

I will try re-running with the -debug option on the additional subjects that had this issue.