Bug in vatsatseg new version?

[lelamuc]

When using the new version of vatsatseg, somehow the python script I used before does not work any more. It gives me the correct output, but the output .nii files do not appear in the directory or in the "real" folder. Did the commands for the python notebook change with the new version?

[lelamuc]

@maxdiefenbach
I looked at the issue with Sophia today and we could not find the reason for the output not appearing in the respective folder.
However we opened the vatsatseg with the Kommandozentrale and the following appeared:

D:\Dokumente_Forschung\Studie- PLIS\PLIS Daten\vatsatsegPLIS>vatsatseg -w IM_00
13_PLIS049BC_4_mDIX_SequenceNumber_702_W.dcm -f IM_0013_PLIS049BC_4_mDIX_Sequenc
eNumber_702_F.dcm -o IM_0013_PLIS049BC_4_mDIX_SequenceNumber_702_labelmap.nii.gz

INFO:vatsatseg.vatsatseg:Read input. ...
INFO:vatsatseg.vatsatseg:Done.
INFO:vatsatseg.vatsatseg:Read labeldescfile. ...
INFO:vatsatseg.vatsatseg:Done.
INFO:vatsatseg.vatsatseg:Start segmentation. ...
d:\programme\python\lib\site-packages\skimage\morphology\convex_hull.py:61: Runt
imeWarning: Mean of empty slice.
offset = coords.mean(axis=0)
d:\programme\python\lib\site-packages\numpy\core_methods.py:73: RuntimeWarning:
invalid value encountered in true_divide
ret, rcount, out=ret, casting='unsafe', subok=False)
Traceback (most recent call last):
File "d:\programme\python\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "d:\programme\python\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "D:\Programme\Python\Scripts\vatsatseg.exe_main.py", line 9, in
File "d:\programme\python\lib\site-packages\click\core.py", line 722, in call
return self.main(*args, **kwargs)
File "d:\programme\python\lib\site-packages\click\core.py", line 697, in main
rv = self.invoke(ctx)
File "d:\programme\python\lib\site-packages\click\core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "d:\programme\python\lib\site-packages\click\core.py", line 535, in invoke
return callback(*args, **kwargs)
File "d:\programme\python\lib\site-packages\vatsatseg\vatsatseg.py", line 48,
in cli
vatsatseg(water, fat, output)
File "d:\programme\python\lib\site-packages\vatsatseg\vatsatseg.py", line 123,
in vatsatseg
labelmap = vatsatseg_3d(w_img, f_img, labeldict)
File "d:\programme\python\lib\site-packages\vatsatseg\vatsatseg.py", line 175,
in vatsatseg_3d
labeldict)
File "d:\programme\python\lib\site-packages\vatsatseg\vatsatseg.py", line 207,
in get_labelmap_2d
vat_mask = get_vat_mask(f_mask, abdominal_water_mask)
File "d:\programme\python\lib\site-packages\vatsatseg\vatsatseg.py", line 368,
in get_vat_mask
vat_mask = convex_hull_image(binary_opening(vat_mask)) & f_mask
File "d:\programme\python\lib\site-packages\skimage\morphology\convex_hull.py"
, line 65, in convex_hull_image
chull = Delaunay(coords).convex_hull
File "qhull.pyx", line 1826, in scipy.spatial.qhull.Delaunay.init
File "qhull.pyx", line 275, in scipy.spatial.qhull._Qhull.init
ValueError: No points given

Maybe this helps with finding the error?

[maxdiefenbach]

I have an idea on what happens. I'll try to fix it this week.

[maxdiefenbach]

@lelamuc Where do I find the same dataset on the NAS?