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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

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Shane Kippenhan
February 09, 2004 05:33PM
Hello,

I'm trying to run 3dVol2Surf with meshes/spec files that are generated as the output of MapIcosahedron on my Redhat 7.3 system.

Apologies in advance for the lengthy message, but I'm hoping more details will result in fewer iterations.

Here's my command line:

3dVol2Surf -spec lh.ICBM_std.spec -surf_A stdSmoothwm -surf_B stdPial -sv ICBM_SurfVol+orig -grid_parent vbm_std+orig -map_func max -f_steps 10 -f_p1_mm -6 -debug 2 -cmask "-a vbm_std+orig -expr step(a-0.1)" -out_1D vol2surf.out

This kind of thing works all the time for me, so the problem seems to have something to do with the specfile contents and/or its surface name conventions. The last few lines of relevant output are as follows:

---------------------excerpted---------------------------

-- select surfs: searching 2 names...
-- select surfs: found name 'stdSmoothwm'
-- select surfs: found name 'stdPial'
-- select surfs: returning 2 names
-- map ref: replace '' with './SAME'
-- map ref: replace '' with './SAME'

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #0/2(Local Domain Parent), loading ...

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #1/2 (mappable via Local Domain Parent), loading ...
++ surfaces loaded.
++ found 0 mappable surfaces
** found 0 mappable surfaces (but expected 2)
No results from 3dVol2Surf

------------------------ end of excerpt ------------------------

My spec file looks like this:

# SUMA_MapIcosahedron-main spec file for lh.ICBM

#define the group
Group = lh.ICBM

#define various States
StateDef = stdSmoothwm
StateDef = stdPial
StateDef = stdInflated
StateDef = stdSphere
StateDef = stdWhite
StateDef = stdSphere.reg

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

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

NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.ICBM_stdInflated.asc
LocalDomainParent = lh.ICBM_stdSmoothwm.asc
SurfaceState = stdInflated
EmbedDimension = 3

NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.ICBM_stdSphere.asc
LocalDomainParent = lh.ICBM_stdSmoothwm.asc
SurfaceState = stdSphere
EmbedDimension = 3

NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.ICBM_stdWhite.asc
LocalDomainParent = lh.ICBM_stdSmoothwm.asc
SurfaceState = stdWhite
EmbedDimension = 3

NewSurface
SurfaceFormat = ASCII
SurfaceType = FreeSurfer
FreeSurferSurface = lh.ICBM_stdSphere.reg.asc
LocalDomainParent = lh.ICBM_stdSmoothwm.asc
SurfaceState = stdSphere.reg
EmbedDimension = 3


What am I doing wrong?

Thanks,

Shane

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Subject Author Posted

3dVol2Surf with standard mesh

Shane Kippenhan February 09, 2004 05:33PM

Re: 3dVol2Surf with standard mesh

rick reynolds February 10, 2004 08:35AM

Re: 3dVol2Surf with standard mesh

Shane Kippenhan February 10, 2004 02:58PM

Re: 3dVol2Surf with standard mesh

rick reynolds February 10, 2004 05:20PM

Re: 3dVol2Surf with standard mesh

Shane Kippenhan February 11, 2004 11:01AM

Re: 3dVol2Surf with standard mesh

rick reynolds February 11, 2004 12:31PM