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MIC-DKFZ / HD-BET

MRI brain extraction tool
Apache License 2.0
255 stars 61 forks source link

'sform' info stripped from output skull-stripped images #10

Closed beaudsy closed 3 years ago

beaudsy commented 4 years ago

Hi Fabian, Great program! Thank you for sharing!

I have been using HD-BET for past few months to skull-strip T1 images, but am now coming up against an "Inconsistent orientation" error using FSL's make_bianca_mask. I linked this to the sform information being stripped from the nifti header in the HD-BET created skull-stripped image (using skull-stripped image from FSL bet which does not remove sform info works perfectly with make_bianca_mask without issue).

I am wondering why HD-BET strips this info and whether there may be plans to prevent this from happening or adding the info back into the output images.

Thanks.

Andrew

FabianIsensee commented 3 years ago

Hi, oh wow I must have overlooked this issue somehow. This problem is related to SimpleITK which HD-BET uses. You should be able to just overwrite the geometry of the resulting segmentations with that of the original image and everything should be fine. Best, Fabian

beaudsy commented 3 years ago

Fabian, Absolutely no problem. Found a work-a-round similar to the one you recommended. Appreciate the reply.

Andrew