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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November 24, 2020 01:02PM
Hi, Ellen-

Glad you found the root of the different matrix problem.

The pipeline I use and recommend for distortion correction, tensor estimation, and more is the AFNI+TORTOISE+FreeSurfer pipeline described in the FATCAT_DEMO2 here:
[afni.nimh.nih.gov]
It goes from start to finish with processing. The TORTOISE tools DIFFPREP and DR_BUDDI perform Gibbs ringing+motion+eddy current distortion correction and EPI distortion correction, respectively. (Performing EPI distortion correction with DR_BUDDI depends on having a dual phase encoded DWI acquisition.)

I am obviously biased, but I think the FATCAT_DEMO2 describes a good road to be on.

Tying with your previous question:
Re. converting FreeSurfer output to NIFTIs and GIFTIs: yes, I would use @SUMA_Make_Spec_FS. That is part of the FATCAT_DEMO2 pipeline. All the outputs from there get brought to diffusion space in the demo pipeline.

I am not familiar with the Nipype align tool, or what it does exactly with diffusion data, unfortunately.

--pt
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