Hey everyone, I am a graduate student new to diffusion MRI processing. I have been using the Camino toolbox to calculate structural connectivity matrices and have run into an error. For some subjects, when I run the conmat function, I get a connectivity matrix of all 0’s with no error message. This happens with both the in the command line and with the nipype wrapper.
Below is a link to a down-sampled version of the .trk tractography files, .Bfloat Camino tractography files, the registered atlases with labels, and the output connectivity matrices. The set of data that is processed successfully by conmat has the header 'Working', while the set that fails has the header 'NotWorking'. The error is reproducible on my end with these down-sampled files.
Link to files: https://www.dropbox.com/sh/sg8u7ev2kg1chtn/AACEpfuv-gArroEa95VwTk6wa?dl=0
Exact commands with camino 9cf8bef17561e88d730df3bc6a8bc111ed1d93aa :
conmat -inputfile WorkingStreamlines.Bfloat -targetfile WorkingRegisteredAtlas.nii.gz -outputroot Working_
conmat -inputfile NotWorkingStreamlines.Bfloat -targetfile NotWorkingRegisteredAtlas.nii.gz -outputroot NotWorking_
Previously completed conversion steps:
trackvis_to_camino -i WorkingStreamlines.trk -o WorkingStreamlines.Bfloat
trackvis_to_camino -i NotWorkingStreamlines.trk -o NotWorkingStreamlines.Bfloat
No error messages are generated.
Any help or tips for what might be going wrong that you could give would be greatly appreciated! Thank you,
-Cooper Mellema