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LittleBrainLab / microbrain

Fully automated whole-brain diffusion MRI analysis of grey matter
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Voxel-based subcortical segmentation breaks on images with different orientation #5

Closed grahamlittlephd closed 2 years ago

grahamlittlephd commented 2 years ago

surf_to_volume_mask will output voxel labels in the incorrect oriention (i.e flipped/rotated) on some data.

This can be fixed by commenting out the following line in surf_util.pyn in the write_image function writer.SetQFac(-1) # TODO: Still unsure why I have to do this but will keep doing it until it doesn't work

Need to figure out why this Qfac needs to be for some diffusion images but not others

Pipeline broke with HCP data input after tractoflow pipeline. Note that regular HCP data as input works fine.

grahamlittlephd commented 2 years ago

Fixed on the following pull request merged into dev

https://github.com/grahamlittlephd/MicroBrain/pull/7