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dke-questions > brain extraction of diffusion images
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Jun 28, 2017 03:06 PM | wafaa sweidan
brain extraction of diffusion images
Hello,
I did eddy current correction for the 4D.nii nifti image of my diffusion weighted images, but when I do brain extraction, the image will be 3d.nii, which I cant use in the dke software. so is skull removal prior to kurtosis estimation a necessity or does not have an effect on results?
I did eddy current correction for the 4D.nii nifti image of my diffusion weighted images, but when I do brain extraction, the image will be 3d.nii, which I cant use in the dke software. so is skull removal prior to kurtosis estimation a necessity or does not have an effect on results?
Jun 28, 2017 08:06 PM | Riccardo De Feo
RE: brain extraction of diffusion images
Hello Wafaa
I take you are talking about FLS for the eddy correction and brain extraction? If I understand what you want to do, you need to generate a mask when you use the brain extraction function, then you can use fslmaths to multiply that mask for every volume in the 4D nifty.
I take you are talking about FLS for the eddy correction and brain extraction? If I understand what you want to do, you need to generate a mask when you use the brain extraction function, then you can use fslmaths to multiply that mask for every volume in the 4D nifty.
Jun 29, 2017 01:06 PM | wafaa sweidan
RE: brain extraction of diffusion images
Hello Ricardo,
Thank you so much for your reply, it helped !
Regards,
Wafaa
Thank you so much for your reply, it helped !
Regards,
Wafaa