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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March 24, 2020 02:48PM
We recently started using the 7T scanner and are having problems with deskulling. The mprage in the directory looks fine but the background noise have values above zero and are different than the 3T data we have been processing. The deskulling is failing and the final image is clearly distorted/warped because of this. The original images in the briks directory are not warped. We are using afni_proc.py to generate the proc for the analysis. How can we modify the deskulling in the generated proc to fix this deskulling problem? Thanks for any help.
Subject Author Posted

Problem with deskulling 7T scan

mikek March 24, 2020 02:48PM

Re: Problem with deskulling 7T scan

ptaylor March 24, 2020 03:19PM

Re: Problem with deskulling 7T scan

mikek March 25, 2020 02:35PM

Re: Problem with deskulling 7T scan

ptaylor March 25, 2020 02:53PM

Re: Problem with deskulling 7T scan

mikek March 25, 2020 03:16PM

Re: Problem with deskulling 7T scan

ptaylor March 25, 2020 04:36PM

Re: Problem with deskulling 7T scan

mikek March 26, 2020 09:00AM

Re: Problem with deskulling 7T scan

ptaylor March 26, 2020 09:35AM

Re: Problem with deskulling 7T scan

mikek March 26, 2020 09:49AM

Re: Problem with deskulling 7T scan

ptaylor March 26, 2020 10:25AM

Re: Problem with deskulling 7T scan

mikek March 26, 2020 01:28PM

Re: Problem with deskulling 7T scan Attachments

mikek March 26, 2020 05:35PM

Re: Problem with deskulling 7T scan

mikek March 27, 2020 08:21AM

Re: Problem with deskulling 7T scan

ptaylor March 27, 2020 09:21AM

Re: Problem with deskulling 7T scan

Colm Connolly March 26, 2020 09:11AM

Re: Problem with deskulling 7T scan

ptaylor March 26, 2020 09:33AM

Re: Problem with deskulling 7T scan

Colm Connolly March 26, 2020 04:53PM

Re: Problem with deskulling 7T scan

ptaylor March 26, 2020 05:17PM