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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eji
November 24, 2020 11:15AM
Hi pt.
I finally figured out why some of those files were on different grids. When I transformed the freesurfer file to AFNI, I used the transformation matrix based on oblique dwi data rather than the de-obliqued (3dWarp) data. Thus, this should solve my problem.

It seems like you suggest that I should not use 3dAllineate. Ok.

Further, our collaborators sent their pipeline for dwi pre-processing (not in AFNI, though). The first step is the equivalent of 3dWarp. However, I didn't perform the equivalent of the last 3 steps in AFNI. Would you suggest I could just use their pre-proprocessed data, or should I do this in AFNI or can I just forget them all?

1. aligning and centering (pnlNipype and ANTS v2.3.4) --- deoblique
2. denoising with dwidenoise (MRtrix3 v3.0.1)
3. unringing with mrdegibbs (MRtrix3 v3.0.1)
4. head motion correction with eddy (FSL v.6.0.1) --- originally I thought 3dAllineate took care of this but now it seems not.
Subject Author Posted

3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

eji October 12, 2020 08:12AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

ptaylor October 12, 2020 09:49AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR Attachments

eji October 21, 2020 06:44AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

ptaylor October 22, 2020 10:54AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR Attachments

eji October 26, 2020 03:04PM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

ptaylor October 27, 2020 08:47AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

eji November 10, 2020 09:35AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

ptaylor November 10, 2020 10:26AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

eji November 10, 2020 11:37AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

ptaylor November 10, 2020 11:59AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

eji November 10, 2020 12:14PM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

eji November 10, 2020 12:34PM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

ptaylor November 10, 2020 12:50PM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

eji November 10, 2020 04:11PM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

ptaylor November 13, 2020 02:50PM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

eji November 14, 2020 03:23AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

eji November 24, 2020 11:15AM

Re: 3dTrackID Fatal Signal 11 (SIGSEGV) + FATAL ERROR

ptaylor November 24, 2020 01:02PM