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WCHN / CTseg

Brain CT image segmentation, normalisation, skull-stripping and total brain/intracranial volume computation.
GNU General Public License v3.0
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How to output only skull removal images? #15

Closed YingJGuo closed 2 years ago

brudfors commented 2 years ago

Hello @GuoCHance

If you want to output only the skull-stripped CT scan and nothing else, setting the spm_CTseg input arguments tc and def to false, and skullstrip to true should do the trick.

YingJGuo commented 2 years ago

thanks a lot !! It works ! But unfortunately, I am still trying to solve the problem "Out of memory"...

brudfors commented 2 years ago

Great you got it working! CTseg can require quite a lot of RAM if your are working on large images. Depending on your aim, a possible solution could be to downsample the CT image by some amount (making sure that the downsampling is encoded in the affine matrix of the nifti header).

YingJGuo commented 2 years ago

Great you got it working! CTseg can require quite a lot of RAM if your are working on large images. Depending on your aim, a possible solution could be to downsample the CT image by some amount (making sure that the downsampling is encoded in the affine matrix of the nifti header).

Thank you for your patient reply. I will try it !