AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Trevor Vincent
July 01, 2009 04:01PM
Hi everybody,

I'd like to try and use AFNI's 3dSkullstrip, which seems like it might work better for brain extraction on non-human heads.

Anyway, I viewed my 3d rodent Nifti-1 images in afni and they look fine but when I run:

3dskullstrip -input in.nii -prefix out.nii -rat

it gives the following warning:
WARNING: NO spatial transform (neither qform nor sform), in NIfTI file

and the 3dskullstrip output image seems to be just a small rectangle. I can upload the input file if needed.

If anyone has had this problem or knows how to remedy it please let me know, it would be greatly appreciated.

Thanks,
Trevor Vincent
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Subject Author Posted

Newbie 3dSkullstrip question

Trevor Vincent July 01, 2009 04:01PM

Re: Newbie 3dSkullstrip question

Trevor Vincent July 01, 2009 06:02PM

Re: Newbie 3dSkullstrip question

bob cox July 01, 2009 09:02PM

Re: Newbie 3dSkullstrip question

Trevor Vincent July 02, 2009 12:11AM