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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rick reynolds
July 29, 2015 09:50AM
Hi Celia,

Maybe the first thing to note is the 3dSkullStrip
merely warned you about the brain being oblique.
There is nothing in that output that suggests it
failed. Did the skull stripping actually work?

If you do want to de-oblique a dataset, then 3dWarp
is the most appropriate way to go. Do not use
3dQwarp, as that is for non-linear registration to
some template (base), but that it not what you seem
to be doing.

The error from 3dWarp just says there is no -source
option. Please do not use it. The "3dWarp -help"
output has an example of -deoblique (-oblique2card).
Please review the help, either with -help or maybe
from the list of all AFNI programs: afni.nimh.nih.gov.


Consider this adjusted command: 

3dWarp -deoblique -prefix deobl-r01_MC r01_MC+orig

But again, maybe 3dSkullStrip worked and you do not
have to de-oblique the data.

- rick
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Subject Author Posted

using 3dWarp?

CeliaG July 29, 2015 08:36AM

Re: using 3dWarp?

CeliaG July 29, 2015 09:17AM

Re: using 3dWarp?

rick reynolds July 29, 2015 09:50AM

Re: using 3dWarp?

CeliaG July 30, 2015 08:00AM