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cheba-nil / CNS

CHeBA NiL Software with UBO Detector to extract white matter hyperintensities
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Failure to create appropriate files if original filename is not <id>_FLAIR.nii #3

Open eldorz opened 4 years ago

eldorz commented 4 years ago

Code is sensitive to original FLAIR image filename.

line 32 of WMHextraction_kNNdiscovery_step1.sh expects ..._FLAIR_seg_ but those output files are named ..._FLAIR_axial_seg when original files are called 001_FLAIR_axial.nii.

Quickstart guide suggests that the filename after _ is not critical. An example 1111_flairABC.nii.gz is given.

Renaming the original images to FLAIR.nii and T1.nii fixes the problem.