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vineetraichur / LiFE_ACNN_Pipeline

Pre-process diffusion data, run tractography and evaluate connectomes
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Issue with output from fiber tracking algorithms #5

Open vineetraichur opened 6 years ago

vineetraichur commented 6 years ago

The mat files produced during step 4 (fiber tracking algorithms) are extremely large in comparison to the tractography mat files in LiFE demo data.

These tractography files are then input to step 5 (LiFE tool) where I encounter this error. tract_file_issue

Looks like the output files from step 4 are not in a format that LiFE tool in step 5 expects them to be. Here's the script that runs all the processes in step 4 - https://github.com/vineetraichur/LiFE_ACNN_Pipeline/blob/master/Step4_Tractography_Sweep/Step4_tract_sweep.sh

Maybe we need to modify some settings when using tracking algorithms from mrtrix. Can you please help?

francopestilli commented 6 years ago

@vineetraichur it looks like the previous step failed or generated improper data. That might be the reason for the NaNs inside the structure. That should not happen.

Does it make sense?

vineetraichur commented 6 years ago

@francopestilli That makes sense. I am sure that Step 4 did not fail, but it is possible that it generated improper data. Nothing in the messages produced during execution points to an error though. Do you have any suggestions on how to troubleshoot in this case?