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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July 04, 2018 04:29PM
Hi, Sondos-

That isn't the format for providing the DTI parameter files. It's described here:
-dti_in  INPREF :basename of DTI volumes output by, e.g., 3dDWItoDT.
                     NB- following volumes are *required* to be present:
                     INPREF_FA, INPREF_MD, INPREF_L1,
                     INPREF_V1, INPREF_V2, INPREF_V3,
                     and (now) INPREF_RD (**now output by 3dTrackID**).
                     Additionally, the program will search for all other
                     scalar (=single brik) files with name INPREF* and will
                     load these in as additional quantities for WM-ROI
                     stats; this could be useful if, for example, you have
                     PD or anatomical measures and want mean/stdev values
                     in the WM-ROIs (to turn this feature off, see below,
                     'dti_search_NO'); all the INPREF* files must be in same
                     DWI space.
                     Sidenote: including/omitting a '_' at the end of INPREF
                     makes no difference in the hunt for files.

So, instead of:
-dti_in /Users/dti-afni_*.nii.gz

I guess you would want:
-dti_in /Users/dti-afni
(though, that looks like you are writing DTI outputs to your /Users/ directory?)

In short, if you want to use dti_FA.nii.gz, dti_MD.nii.gz, etc., then provide "-dti_in dti"-- just the prefixes without extensions.

--pt
Subject Author Posted

3dTrackID

sondosayyash July 04, 2018 03:13PM

Re: 3dTrackID

ptaylor July 04, 2018 04:29PM

Re: 3dTrackID

sondosayyash July 04, 2018 10:13PM

Re: 3dTrackID

ptaylor July 05, 2018 08:40AM

Re: 3dTrackID

sondosayyash July 05, 2018 12:37PM

Re: 3dTrackID

ptaylor July 05, 2018 01:44PM

Re: 3dTrackID Attachments

sondosayyash July 05, 2018 02:44PM

Re: 3dTrackID

ptaylor July 05, 2018 03:04PM

Re: 3dTrackID Attachments

sondosayyash July 09, 2018 09:55AM

Re: 3dTrackID

ptaylor July 09, 2018 11:45AM

Re: 3dTrackID

sondosayyash August 14, 2018 03:07PM

Re: 3dTrackID

ptaylor August 14, 2018 04:45PM

Re: 3dTrackID

sondosayyash August 14, 2018 04:56PM

Re: 3dTrackID

ptaylor August 14, 2018 05:49PM

Re: 3dTrackID

sondosayyash August 15, 2018 04:55PM