With VTK 9, not VTK 8, merge-surfaces doesn't create the divider correctly. The cutting plane is in the correct location but the divider polygon is in the wrong spot (the vertices in the left hemisphere away from the cutting plane). See screen shots.

The lh / rh label definitions are hard-coded in recon-neonatal-cortex.py and could be made user-defineable like the labels are. otherwise for instance the automatic hemisphere splitting does not work with user-defined labels.

I'm getting this error in deform-mesh:

Assertion pos2 == extrema.end() || (pos2+1 != extrema.end() && !pos2->min && pos2->idx < (pos2+1)->idx && (pos2+1)->min) failed in /home/addo/dev/MCRIBS/MIRTK/MIRTK/Packages/Deformable/src/ImageEdgeDistance.cc line 1791: pos2 is a valid edge interval start

What should I be looking for to debug it?

Thanks.

In the first surface that is created, the “cerebrum” surfaces, if you have fast collision OFF it prevents the surface from having the high curvature it needs to penetrate into deep sulci. In addition, there are some cases where shocks form in the surface (a shock is where you have a V shape in a surface and the faces at the V apex cross over) and you get this spike that stays outside the brain because the collision detection prevents the vertices at the shock moving. When fast collision is turned ON for the cerebrum surface it doesn’t have this issue and it penetrates correctly.

For the “white” and “pial” surfaces you do need to have the fast collision OFF to prevent those errors you are having. There do seem to still be shocks forming for the “pial” surfaces which is why you get these “pointy” regions of pial surface at the fundi of sulci sometimes. I might need to alter the parameters to make the outward movement of the pial surface change so these shocks don’t form. It is possible that you are getting better results with fast collision off because it has fewer restrictions on curvature and overlapping faces. But the problem is that it causes some crashes due to said overlapping faces.

Any ideas for changing the parameters to prevent shocks?

• ComputeEdgeLengthRange
• UpdateImplicitSurfaceDistance

Using the default recon-neonatal-cortex script with default options except for -ensure-pial-is-outside-white-surface and the white and pial surfaces are not in correspondence. The surfaces are in the correct locations but face configuration differs between white and pial. This happens both in the dual-hemisphere and split surfaces. Any thoughts? Thank you in advance.

The factory for local optimisers has no registered optimiser types. Probably a missing link dependency. The optimisers provided by the Deformable module are not auto-registered.

I'm getting a (rare) error where there is a cerebrum hull surface outside the bounds of the corpus callosum mask. I was able to fix it by padding the regions.nii.gz image slightly by a few voxels. I have put some code into MIRTK and Deformable to fix it. I have attached a patch file that contains the fix.
padregions.patch.txt

Error: Surface outside bounds of input image: .../temp/corpus-callosum-mask.nii.gz
Traceback (most recent call last):
File "/opt/MCRIBS/bin/../MIRTK/MIRTK-install/lib/tools/recon-neonatal-cortex", line 916, in
use_fast_collision = args.fastcollision)
File "/opt/MCRIBS/bin/../MIRTK/MIRTK-install/lib/tools/recon-neonatal-cortex", line 550, in recon_neonatal_cortex
corpus_callosum_mask=corpus_callosum_mask, temp=temp_dir, use_fast_collision=use_fast_collision)
File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/deformable/neonatal_cortex.py", line 1083, in recon_cortical_surface
out1 = push_output(stack, add_corpus_callosum_mask(hull, mask=corpus_callosum_mask, oname=out1))
File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/deformable/neonatal_cortex.py", line 558, in add_corpus_callosum_mask
project_mask(iname, oname, mask, name='ImplicitSurfaceFillMask', dilation=20, invert=True)
File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/deformable/neonatal_cortex.py", line 447, in project_mask
opts={'labels': mask, 'fill': fill, 'dilation-radius': dilation, 'name': name})
File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/deformable/neonatal_cortex.py", line 167, in run
_run(tool, args=args, opts=opts, showcmd=showcmd, threads=threads)
File "/opt/MCRIBS/MIRTK/MIRTK-install/lib/python/mirtk/subprocess.py", line 296, in run
raise e

The current output is rather useless.

The help output of deform-mesh currently does not include many of the available options.

I'm having an issue with the reconstruction. I end up with a non-closed surface and all the boundary edges are on the midline where the two cerebral surfaces connect (see attached for the regions.nii.gz file with the cerebrum-1.vtp surface overlaid and the boundary edges in white dots). I'm not sure how to address this?

Thanks in advance.

I am trying to use "calculate-surface-spectrum" which is requiring that "Numerics module was built with ARPACK and UMFPACK". (on Ununtu 14.04)

However when trying to build and install mirtk with above options, running into below issues.

make[2]: *** [Packages/Deformable/src/CMakeFiles/LibDeformable.dir/ImageEdgeDistance.cc.o] Error 1
make[1]: *** [Packages/Deformable/src/CMakeFiles/LibDeformable.dir/all] Error 2

.....
request for member ‘insert’ in ‘extrema’, which is of non-class type ‘mirtk::ImageEdgeDistanceUtils::ComputeDistances::Extrema {aka int}’
r = extrema.insert(r, mid);
......

ImageEdgeDistance.cc:1355:28: note: mismatched types ‘_Tp [_Nm]’ and ‘int’
for (auto &&extremum : extrema) {

Can you please assist.

The fast collision test used to reconstruct the WM surface was determined by @amakropoulos to cause issues with the cortical thickness measures. Best to disable this option.