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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June 03, 2018 01:50PM
Hi-

Did you try just running deterministic ("-mode DET") tracking first? As noted in the help/scripts, probabilistic tracking methods for HARDI data rely on very heuristic uncertainty measures at the moment.

Also, I am not sure what a recommended threshold value for GFA would be-- basically, voxels with GFA values above that threshold are considered in the WM, and therefore tracked, while those below it are excluded from tracking. In the DTI case of having just FA, for adult humans a threshold value of FA>0.2 is typically taken across the field as a good proxy for WM; in human infants, FA>0.1 is often used. For GFA, I am not sure if such a threshold applies-- that is worth investigating in papers that track that kind of HARDI reconstruction method. You can investigate what would be a good value in your data by adjusting the threshold and seeing what looks like a good WM map.

--pt
Subject Author Posted

How to correct DWI EPI distortion with only one b value PA volume? Attachments

EXP.2086 May 02, 2018 10:20PM

Re: How to correct DWI EPI distortion with only one b value PA volume?

ptaylor May 03, 2018 05:59AM

Re: How to correct DWI EPI distortion with only one b value PA volume? Attachments

EXP.2086 May 03, 2018 08:57AM

Re: How to correct DWI EPI distortion with only one b value PA volume?

ptaylor May 03, 2018 01:03PM

Re: How to correct DWI EPI distortion with only one b value PA volume? Attachments

EXP.2086 May 04, 2018 04:33AM

Re: How to correct DWI EPI distortion with only one b value PA volume?

ptaylor May 04, 2018 08:11AM

Re: How to correct DWI EPI distortion with only one b value PA volume? Attachments

EXP.2086 May 24, 2018 11:49AM

Re: How to correct DWI EPI distortion with only one b value PA volume?

ptaylor May 30, 2018 09:38AM

Re: How to correct DWI EPI distortion with only one b value PA volume? Attachments

EXP.2086 May 25, 2018 12:58PM

Re: How to correct DWI EPI distortion with only one b value PA volume?

ptaylor May 30, 2018 10:17AM

Re: How to correct DWI EPI distortion with only one b value PA volume? Attachments

EXP.2086 June 02, 2018 03:39AM

Re: How to correct DWI EPI distortion with only one b value PA volume?

ptaylor June 03, 2018 01:50PM

Re: How to correct DWI EPI distortion with only one b value PA volume?

EXP.2086 May 24, 2018 12:06PM

Re: How to correct DWI EPI distortion with only one b value PA volume?

ptaylor May 30, 2018 10:18AM