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

History of AFNI updates  

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May 01, 2023 11:37AM
With a mask dataset as input, you would not use the -init_skullstr_off option. See the example 3 in the current @SSwarper help for how to use an external mask dataset as input. The mask provides a replacement for the initial skullstripping step. Voxels included in that mask should be included in the output datasets. The default nonlinear warping in afni_proc.py will work too, but it's a little different because of the skullstripping in @SSwarper and the default affine alignment in step.
Subject Author Posted

3dWarp -deoblique problem

zcui12 March 28, 2023 08:14PM

Re: 3dWarp -deoblique problem

ptaylor March 28, 2023 08:57PM

Re: 3dWarp -deoblique problem

Daniel Glen March 29, 2023 10:02AM

Re: 3dWarp -deoblique problem Attachments

zcui12 April 03, 2023 03:22PM

Re: 3dWarp -deoblique problem

ptaylor April 03, 2023 04:46PM

Re: 3dWarp -deoblique problem

zcui12 April 04, 2023 12:42PM

Re: 3dWarp -deoblique problem

ptaylor April 04, 2023 01:00PM

Re: 3dWarp -deoblique problem

zcui12 April 04, 2023 05:39PM

Re: 3dWarp -deoblique problem

ptaylor April 04, 2023 10:44PM

Re: 3dWarp -deoblique problem Attachments

zcui12 April 16, 2023 07:00PM

Re: 3dWarp -deoblique problem/skull-strip & Anatomy-EPI alignment issue Attachments

zcui12 April 16, 2023 07:09PM

Re: 3dWarp -deoblique problem/skull-strip & Anatomy-EPI alignment issue

Daniel Glen April 17, 2023 03:49PM

Re: 3dWarp -deoblique problem/skull-strip & Anatomy-EPI alignment issue

zcui12 May 01, 2023 10:22AM

Re: 3dWarp -deoblique problem/skull-strip & Anatomy-EPI alignment issue

Daniel Glen May 01, 2023 11:37AM

Re: 3dWarp -deoblique problem/skull-strip & Anatomy-EPI alignment issue Attachments

zcui12 May 04, 2023 02:15PM

Re: 3dWarp -deoblique problem

Daniel Glen April 04, 2023 03:35PM

Re: 3dWarp -deoblique problem

zcui12 April 04, 2023 05:58PM

Re: 3dWarp -deoblique problem

Daniel Glen April 04, 2023 06:37PM