SUMA brain turns completely green when 't' is pressed allowing SUMA and AFNI to communicate

AFNI Message Board
1

I am trying to display AFNI data on a SUMA surface but keep running into the issue that sometimes the correct data will display for a second and then the SUMA surface becomes totally highlighted with a bright green color. I’ve looked at the difference with output from a correctly working example and noticed several differences:

  1. The number of Nodes, Normals and Triangles is much smaller (one-sixth of the working example)
  2. There is a switch underlay command that is sent
  3. There is a forced switch from ‘Tailarach View’ to ‘Original View’

I’ve included the terminal output below. I have changed the text color for the significant differences I listed above. I hope the question and output is clear. Please let me know if you need any clarfication.

Thank you so much,
Vicki

Here is the output:
Suma -spec ~/SUMA/std.60.subject_lh.spec -sv ~/SUMA/subject_SurfVol.nii
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #1/7(Local Domain Parent), loading
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #2/7 (mappable via Local Domain Parding …
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #3/7 (mappable via Local Domain Parding …
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #4/7 (mappable via Local Domain Parding …
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #5/7 (mappable via Local Domain Parding …
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #6/7 (mappable via Local Domain Parding …
vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #7/7 (mappable via Local Domain Parding …
SUMA_Engine: Starting to listen …
SUMA_niml_call: Contacting on tcp:localhost:53211 (0), maximum wait 2.0
(You can change max. wait time with env. SUMA_DriveSumaMaxWait)
SUMA_niml_call: Trying local connection…
++ NIML connection opened from 127.0.0.1 (tcp:host:53211,AFNI_SUMA_NIML

SUMA_Engine: Sending surface std.60.lh.smoothwm.gii (NodeList, FaceSetLNormList)…

+++ NOTICE: SUMA_ixyz: received 36002 nodes
for surface std.60.lh.smoo (#0),
session ~/subjectDataFolder/
I/O time = 20 ms, Processing = 1 ms

+++ NOTICE: 36002 normals attached
to surface std.60.lh.smoo (#0),
session ~/subjectDataFolder/
I/O time = 3 ms, Processing = 1 ms
SUMA_Engine: Sending surface std.60.lh.pial.gii (NodeList, FaceSetList,List)…

+++ NOTICE: SUMA_ijk: 72000 triangles attached
to surface std.60.lh.smoo (#0),
session ~/subjectDataFolder/
I/O time = 6 ms, Processing = 1 ms

+++ NOTICE: SUMA_ixyz: received 36002 nodes
for surface std.60.lh.pial (#1),
session ~/subjectDataFolder/
I/O time = 5 ms, Processing = 1 ms

+++ NOTICE: 36002 normals attached
to surface std.60.lh.pial (#1),
session ~/subjectDataFolder/
I/O time = 8 ms, Processing = 1 ms
SUMA_Engine: Sending surface std.60.lh.white.gii (NodeList, FaceSetListmList)…

+++ NOTICE: SUMA_ijk: 72000 triangles attached
to surface std.60.lh.pial (#1),
session ~/subjectDataFolder/
I/O time = 20 ms, Processing = 1 ms

+++ NOTICE: SUMA_ixyz: received 36002 nodes
for surface std.60.lh.whit (#2),
session ~/subjectDataFolder/
I/O time = 8 ms, Processing = 1 ms

+++ NOTICE: 36002 normals attached
to surface std.60.lh.whit (#2),
session ~/subjectDataFolder/
I/O time = 9 ms, Processing = 0 ms
SUMA_Engine: Sending switch underlay command to (SWITCH_UNDERLAY A.infaol.nii 0)…

+++ NOTICE: SUMA_ijk: 72000 triangles attached
to surface std.60.lh.whit (#2),
~/datafile/
I/O time = 19 ms, Processing = 1 ms

received too many surfaces for LDP ‘std.60.lh.smoothwm.gii (via SAME)’
using surf #0 : std.60.lh.smoothwm.gii
using surf #1 : std.60.lh.pial.gii
ignoring surf #2 : std.60.lh.white.gii
Warning shown intermittenlty.

*+ WARNING: Forced switch from ‘Talairach View’ to ‘Original View’ [#1]

received too many surfaces for LDP ‘std.60.lh.smoothwm.gii (via SAME)’
using surf #0 : std.60.lh.smoothwm.gii
using surf #1 : std.60.lh.pial.gii
ignoring surf #2 : std.60.lh.white.gii
Warning shown intermittenlty.

AFNI cross hair notice:
From Afni:
Surface: std.60.lh.pial.gii
Node: 33586, XYZ: -3.00 15.00 20.00
In Controller [A]:
Surface: std.60.lh.smoothwm.gii, adopted: std.60.lh.smoothwm.gii
Node: 33586, XYZ: -3.00 15.00 20.00

AFNI cross hair notice:
From Afni:
Surface: std.60.lh.pial.gii
Node: 33586, XYZ: -3.50 15.50 20.50
In Controller [A]:
Surface: std.60.lh.smoothwm.gii, adopted: std.60.lh.smoothwm.gii
Node: 33586, XYZ: -3.50 15.50 20.50

2

The output from suma and afni are mixed here. In the afni GUI, the overlay and the underlay must have matching “views”, the +orig or +tlrc part of the AFNI format name. For NIFTI datasets, that view is set by the sform_code in the header. If it doesn’t match between underlay and overlay datasets, the underlay or overlay dataset is switched to match the view of the last selected one. You can work around some of this confusion by

  1. Use AFNI format datasets and/or refit the view and the space with 3drefit.
  2. Set AFNI_NIFTI_VIEW to the desired view type (tlrc or orig)

The colors are sent from the afni GUI based on what is being shown in the afni GUI’s overlay. With typical unthresholded data and default pos/neg scaling with values around zero, most voxels are shown in green, and consequently suma shows the voxels also in green. It’s also possible suma’s GUI may be showing another niml dataset. Switch among surface datasets in the surface object controller (ctrl-s) in the lower left of that controller menu. The ‘1’ check box will only show the currently selected coloring set if that is set. Switch among the coloring set with the “Switch dset” button.

3

Hello, Daniel!

Thank you so much for your reply. I’m sorry it took me so long to find your reply, I’m still new to the AFNI message boards. I’m looking into all of your suggestions.

Thanks Again,
Vicki

4

Thank you, Daniel!

Exploring your suggestions, I found out that I can re-define the overlay after SUMA and AFNI begin communicating and see the desired results on the SUMA surface.

Thanks, Again!
Vicki