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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May 08, 2006 01:00PM
Now that I'm able to view caret rendered volumes in SUMA (thanks Ziad), I find that I still can't do what I set out to do: mapping functional data from afni onto these. What I need to be able to do, if I understand correctly, is somehow assemble a spec file along the lines of what is created with either of the SUMA_make_spec scripts. Since these don't appear to work with caret data, I think I may have to create it from scratch. (Though maybe it's possible to adapt the surefit script to caret data, since caret is supposed to be using surefit for its segmentation anyhow.) For the sake of completeness, let me see if I can give you some background:

This is the method I'm currently using to visualize the data. Apparently I'm not passing a .param file to it properly this way, hence the error.

fmriuser@d109-student:/mnt/data/ron_meyer/Caret_RM/rm20may05a$ suma -i_SF Human.CaretTest.R.Fiducial.2006-03-14.53373.coord Human.CaretTest.R.CLOSED.2006-03-14.53373.topo -sv 3dAnat_Cody

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #1/1(Local Domain Parent), loading ...
Error SUMA_Load_Surface_Object_eng: Volume Parent specified without .param file.
Parent Volume Alignment will not be done.

It subsequently won't link to afni. I am not by any means opposed to hand-crafting a spec file, but when I tried to peanut butter something workable together by looking at a sample SUMA spec, I didn't have any luck. Sorry to trouble you so often, but I'm very close to being able to do what I want to do with these, which would bring great joy to many.

Thanks for your help so far, and I hope that you can help me with this part.

-Cody
Subject Author Posted

Making SUMA Spec File for Caret Volume

Cody May 08, 2006 01:00PM

Re: Making SUMA Spec File for Caret Volume

Ziad Saad May 08, 2006 02:02PM

Re: Making SUMA Spec File for Caret Volume

Cody May 08, 2006 02:21PM

Re: Making SUMA Spec File for Caret Volume

Ziad Saad May 08, 2006 03:26PM

Re: Making SUMA Spec File for Caret Volume

Cody May 10, 2006 02:58PM

Re: Making SUMA Spec File for Caret Volume

Ziad Saad May 10, 2006 04:17PM

Re: Making SUMA Spec File for Caret Volume

Donna Dierker May 11, 2006 09:16AM

Re: Making SUMA Spec File for Caret Volume

Cody May 11, 2006 10:00AM

Re: Making SUMA Spec File for Caret Volume

Cody May 17, 2006 07:52AM

Re: Making SUMA Spec File for Caret Volume

Ziad Saad May 17, 2006 09:57AM

Re: Making SUMA Spec File for Caret Volume

Ziad Saad May 17, 2006 05:03PM

Re: Making SUMA Spec File for Caret Volume

Cody May 18, 2006 07:55AM