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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December 14, 2015 09:41AM
Hi ptaylor,

Yes, this is what I'm wanting. I just followed your steps, and can open the Walnut Brain. I'm still having issues opening a tract on top of this brain though.

Here are the steps I took to try to get the tract open on this brain:

1) Obtain .nii.gz file in FSL.
2) Use IsoSurface to obtain a .ply file.
--This will open in SUMA in 3D, and the Xhair info says 0, 0, 0
3) Use the below code to open both the walnut brain and the tract.

suma -spec TT_N27 -i_ply tract.ply

4) The above code opens the walnut brain. The tract.ply file is viewable in the surface controller panel, but does not appear in the SUMA window. The Xhair info says -

The only difference I can see between opening the tract.ply file alone and with the walnut brain is the Xhair info displaying different values. Is there something I'm missing? Did I do the necessary steps to get a *.nii.gz file to a *ply file?

Thanks for all the help!
Derek Archer
Subject Author Posted

Displaying 3d ROI in SUMA

archerdb December 09, 2015 03:46PM

Re: Displaying 3d ROI in SUMA

ptaylor December 09, 2015 05:22PM

Re: Displaying 3d ROI in SUMA

archerdb December 10, 2015 09:18AM

Re: Displaying 3d ROI in SUMA

ptaylor December 10, 2015 09:37AM

Re: Displaying 3d ROI in SUMA

archerdb December 10, 2015 10:23AM

Re: Displaying 3d ROI in SUMA

ptaylor December 10, 2015 10:50AM

Re: Displaying 3d ROI in SUMA

archerdb December 10, 2015 01:01PM

Re: Displaying 3d ROI in SUMA

ptaylor December 10, 2015 06:15PM

Re: Displaying 3d ROI in SUMA

archerdb December 11, 2015 03:19PM

Re: Displaying 3d ROI in SUMA

ptaylor December 11, 2015 05:08PM

Re: Displaying 3d ROI in SUMA

archerdb December 14, 2015 09:41AM

Re: Displaying 3d ROI in SUMA

ptaylor December 14, 2015 10:42AM

Re: Displaying 3d ROI in SUMA

archerdb December 14, 2015 11:56AM

Re: Displaying 3d ROI in SUMA

ptaylor December 14, 2015 12:35PM

Re: Displaying 3d ROI in SUMA

archerdb December 15, 2015 02:15PM

Re: Displaying 3d ROI in SUMA

ptaylor December 16, 2015 04:13PM

Re: Displaying 3d ROI in SUMA

archerdb December 16, 2015 05:41PM