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MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
http://micapipe.readthedocs.io
GNU General Public License v3.0
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Results from auto_tract #55

Closed HEEHWANWANG closed 1 year ago

HEEHWANWANG commented 1 year ago

Hi, I'm using auto_tract standalone pipeline to do bundle segmentation with whole-brain tractogram we estimated before. Tractograms were estimated with matrix3 iFOD2. When I run auto_tract pipeline, however, there were no streamline counted as Fornix of both hemisphere. I think it is weird because when I open tractogram files, there were streamlines on the Fornix Are there any tips or cautions I need to know for running auto_tract pipeline?

ajschadler12 commented 1 year ago

How does the global tractogram look? You can keep it for some runs by specifying micapipe <subject_args> -SC -keep_tck. My only other suggestion would be to inspect the distortion correction. @rcruces , can you advise on how to check the registration between the diffusion data and the auto-tract template?

rcruces commented 1 year ago

I will close this issue due to lack of response if you have further inquires please don't hesitate to open a new one.