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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October 19, 2004 04:16PM
hi rick, ziad--

let me preface by saying that i have no problems seeing activity with another subject, although i get the same message and have all my surfaces included in that spec file.

i edited the problematic spec so that i only have my smoothwm and flatmap, and toggling See Overlay gets the activity onto the surface w/o the error about LDP--but i get very little of my activity onto the surface. Also, there is no outline of my smoothwm in my SurfVol_Alnd_Expvol.

With the other subject, which works, i get an outline around the smoothwm and pial boundaries, getting alot of the activty i'd like on to the brain. can i make this happen with my problem subject? otherwise, i lose a hell of a lot of activity.

i get a link receipt error for each surface, stating the following:

SUMA_ijk surface dataset idcode is XYZ_1T1... Can't find this in AFNI
SUMA_node_normals surface dataset idcode is XYZ_1T1... Can't find this in AFNI

i modified my spec file as follows:
__________________________________________________________
# define the group
Group = db

# define various States
StateDef = smoothwm
StateDef = pial
StateDef = inflated
StateDef = patch.3d
StateDef = patch.flat
StateDef = sphere
StateDef = qsphere

NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.smoothwm.asc
LocalDomainParent = SAME
SurfaceState = smoothwm
EmbedDimension = 3


NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.patch.flat.asc
LocalDomainParent = lh.smoothwm.asc
SurfaceState = patch.flat
EmbedDimension = 2
___________________________________________________________

i also tried including 3 surfaces in my spec--smoothwm, pial, and flatmap using the smootwhm as the LDP for all three.

again, i do not get the LDP error message, but the activity looks very strange. looks like speckles of activity stretched out along my surface (if you can picture that). also, i don't get the outline of the whitematter/graymatter borders.

also, when i toggle See Overlay, i get the following message:
Error SUMA_process_NIML_data: nel idcode is not found in DOv
Error SUMA_niml_workproc: Failed in SUMA_process_NIML_data

in sum, let me state what i hope to do, and you let me know iif this is possible:
show activity on my flatmap existing between the smoothwm and graymatter borders.

Subject Author Posted

warning, too many surfaces for LDP

Kevin DeSimone October 19, 2004 02:48PM

Re: warning, too many surfaces for LDP

Ziad S. Saad October 19, 2004 03:31PM

Re: warning, too many surfaces for LDP

rick reynols October 19, 2004 03:35PM

Re: warning, too many surfaces for LDP

Kevin DeSimone October 19, 2004 04:16PM

Re: warning: different # nodes

rick reynols October 19, 2004 03:49PM

Re: warning: different # nodes

Kevin DeSimone October 19, 2004 04:33PM

Re: warning: different # nodes

rick reynols October 19, 2004 04:40PM

Re: warning: different # nodes

Ziad S. Saad October 19, 2004 05:16PM

Re: warning: different # nodes

Kevin DeSimone October 20, 2004 10:44AM

Re: warning: different # nodes

Ziad S. Saad October 20, 2004 12:57PM

Re: warning: different # nodes

Kevin DeSimone October 20, 2004 02:38PM

Re: warning: different # nodes

Kai Schreiber December 12, 2004 08:20PM