how to do fslreorient2std in batches?

CCI-Bonn / HD-GLIO

Automated deep-learning based brain tumor segmentation on MRI

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how to do fslreorient2std in batches? #10

Open TSbme opened 1 year ago

TSbme commented 1 year ago

Doing fslreorient2std for every single file is too slow. how to do fslreorient2std in batches?

FabianIsensee commented 1 year ago

Honestly this is a question best asked to the FSL people as this is nothing within our control. If you want to run fslreorient2std for multiple files at once, do the following (requires more CPU cores):

fslreorient2std T1.nii.gz T1_reorient.nii.gz &
fslreorient2std CT1.nii.gz CT1_reorient.nii.gz &
fslreorient2std T2.nii.gz T2_reorient.nii.gz &
fslreorient2std FLAIR.nii.gz FLAIR_reorient.nii.gz &
wait

Best, Fabian