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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September 11, 2019 03:54PM
Hi-

I see that is, indeed, an oversight in being defined in the program's help-- I will add that.

It is the output of including "-debug_briks" in 3dDWItoDT: calculating chi-square results, for goodness-of-(tensor)-fit measures. So, yes, it can be useful for QCing.

Here is the detailed description of its brick values, from 3dDWItoDT's help:
-debug_briks = add sub-briks with Ed (error functional), Ed0 (orig.
                  error), number of steps to convergence and I0 (modeled B0
                  volume).
                  [May, 2017] This also now calculates two goodness-of-fit
                  measures and outputs a new PREFIX_CHI* dset that has two
                  briks:
                     brik [0]: chi^2_p,
                     brik [1]: chi^2_c.
                  These values are essentially calculated according to
                  Papadakis et al. (2003, JMRI), Eqs. 4 and 3,
                  respectively (in chi^2_c, the sigma value is the
                  variance of measured DWIs *per voxel*). Note for both
                  chi* values, only DWI signal values are used in the
                  calculation (i.e., where b>THR; by default,
                  THR=0.01, which can be changed using '-bmax_ref ...').
                  In general, chi^2_p values seem to be <<1, consistent
                  with Papadakis et al.'s Fig. 4; the chi^2_c values are
                  are also pretty consistent with the same fig and seem to
                  be best viewed with the upper limit being roughly =Ndwi
                  or =Ndwi-7 (with the latter being the given degrees
                  of freedom value by Papadakis et al.)

--pt
Subject Author Posted

Updated features/functionality of DTI processing

ptaylor May 04, 2016 03:45PM

Re: Updated features/functionality of DTI processing

ptaylor May 04, 2016 04:55PM

Re: Updated features/functionality of DTI processing

ptaylor May 05, 2016 08:45AM

Re: Updated features/functionality of DTI processing

ptaylor June 13, 2016 01:39PM

Re: Updated features/functionality of DTI processing

ptaylor July 02, 2016 02:17AM

Re: Updated features/functionality of DTI processing

Matthew Hoptman September 11, 2019 01:34PM

Re: Updated features/functionality of DTI processing

ptaylor September 11, 2019 03:54PM