Comments (8)
That message is in the surface file reading code. Can you provide a file that causes such an error, so we can check whether the file truly has zeros in the triangle array?
from workbench.
Yes, surface files are in this zipped folder (along with other relevant fmriprep outputs): https://drive.google.com/file/d/1m2bPZGHVwPN8l9Aehx2Hjhf2PBC5p1Tv/view
The file I was working on specifically is sub-047EPKL011005_ses-1_hemi-L_midthickness.surf.gii
. If there is a more convenient way for me to share these files let me know.
Thank you for the quick response,
Steven
from workbench.
Also note that we use 164k surfaces in the HCP pipelines with wb_command and wb_view, without such an error:
fsaverage.L_LR.spherical_std.164k_fs_LR.surf.gii
See if that makes it through your code without errors.
from workbench.
What files get used for the spheres in the resampling command?
from workbench.
That is a good question, I have made the developers of ciftiTools aware of this, and it is possible that it is an error in how their wrapper function handles files. Their function e.g., resample_surf(surf=surface_fname, resamp_res = 32492, hemisphere='left')
only takes in a single surface and resampling resolution argument, so I am not sure what gets used for spheres.
Thank you for linking me to the surface you use. Unfortunately I got the same error
While running:
/rdma/vast-rdma/vast/gablab/smeisler/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -surface-resample /tmp/Rtmp49kVVm/to_resample.surf.gii /tmp/Rtmp49kVVm/sphereL_158681.surf.gii /tmp/Rtmp49kVVm/sphereL_32492.surf.gii BARYCENTRIC /tmp/Rtmp49kVVm/to_read.surf.gii
ERROR: NAME OF FILE: to_resample.surf.gii
PATH TO FILE: /tmp/Rtmp49kVVm
Vertex used twice in one triangle: triangle 199497, vertex 0Vertex used twice in one triangle: triangle 199498, vertex 0..........
Perhaps it is the writing / reading from tmp
that is causing problems (I am on an HPC without root privileges). I will continue to investigate.
Best,
Steven
from workbench.
158681 is the resolution of your surfaces, not of the sphere I pointed you to, so I don't know why the wrapper is running that command, or what to_resample.surf.gii is supposed to be a copy of. I would guess that it is internally finding the sphere files associated with the subject, and therefore can't resample anything that doesn't match that subject's resolution anyway.
from workbench.
I wonder if it would be better to try using the wb_command -surface-resample directly? While I met the author of ciftitools once, we don't have an established relationship with her to support her tools. Also it's entirely possible that the wrappers are not doing what we would recommend in any case.
from workbench.
Seems reasonable, thank you both. I'll close this because it doesn't seem to be an issue with workbench.
from workbench.
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