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demianw / tract_querier

Implementation of the White Matter Query Language and associated tools for dMRI white matter tract extraction and analysis
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Atlas dissection #50

Open ioannispappas322 opened 1 year ago

ioannispappas322 commented 1 year ago

Hi there.

I am trying to dissect this whole brain .trk to extract the posterior parts of the Cingulum tract.

https://figshare.com/articles/dataset/Advanced_Atlas_of_80_Bundles_in_MNI_space/7375883 This is a dataset to be used by the RecoBundles algorithm to automatically extract anatomically relevant bundles from tractograms.

However when I run something like tract_querier -a MNI152_wmparc_1mm_small.nii.gz -t whole_brain_MNI.trk -q script.qry -o result3 I am getting this error

ValueError: Tracts in the tractography must have at least 2 points tract #420 has less than two points. You can use the tract_math tool to prune short tracts and solve this problem.

I would deeply appreciate any ideas. Everything works fine IIT2mean.trk

Best wishes, Ioannis