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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April 17, 2023 03:49PM
Looks like you have made good progress. The initial skull stripping in @SSwarper is mildly aggressive by default, but it combines with the template alignment to create something more filled in. You can dilate the skullstrip mask or even manually fix the mask and feed that back into a 2nd run through of @SSwarper. You can change the options for the 3dSkullstrip command used in @SSwarper with -SSopt. Alternatively, 3dSkullstrip separately to create the mask and use that as input.
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