Hi,

Regarding the 1) from before..

2.  Is there a way to show GLM Feat results in a vtk mesh object in
>> the3d viewer.  i.e. we have results in the amygdala and would like to
create
>> a 3d mesh object from the resulting activation.  Or overlay this
>> activation in 3d on top of a vtk mesh object.
>>

I was mistaken from my previous response, I was thinking of a function
that does the opposite (projects mesh scalars into an image).

run_mesh_utils --doSampleMesh -m surface.vtk -i statistic.nii.gz -o
surface_with_statistic.vtk

Will interpolate the image value at the precise vertex points (will not
give what you want if stats are not on the boundary of the amygdala). A
work around could be to dilate the stats image before the sampling.
Otherwise, do a combination of image planes and surface.



> bash-3.00$ sed -n '1,3p' <14-L_Accu_first>
> bash: syntax error near unexpected token `newline'
> bash-3.00$ sed -n '1,3p' <14-L_Accu_first.vtk>

Sorry, I was unclear, the command should look like this  "sed -n '1,3p'
14-L_Accu_first.vtk"

I suspect that because there are no scalars associated with the mesh it
simply renders as grey.
You could append scalars using to volume (though I don't have a tool to do
that), is straight forward with ASCII files though. You would then have to
fiddle with the built in colour map to get the desired colour. This is
tricky to get the desired results in FSLview (more so if your have
multiple surfaces).

Alternatively, I have a OpenGL viewer where you can edit surface
properties (i.e. colour, material) for multiple surfaces, and use image
plane for images. If you're using OSX and you're interested I can send you
a link. It's still in development but has quite a bit of functionality.

Cheers,

Brian










> Brian -
>
> I attempted the command to no avail:
>
> *Here is an ls on the directory:*
>
> 14-L_Hipp_first.bvars  first.e26463.6         first_post.o20367.1
> 14-L_Hipp_first.vtk    first.e26463.7         first_post.o22072.1
> 14-L_Late_first.bvars  first.e26463.8         first_post.o24892.1
> 14-L_Late_first.vtk    first.e26463.9         first_post.o27806.1
> 14-L_Pall_first.bvars  first.e29362.1         first_post.o28227.1
> 14-L_Pall_first.vtk    first.e29362.10        first_post.o30580.1
> 14-L_Puta_first.bvars  first.e29362.11        first_post.o32433.1
> 14-L_Puta_first.vtk    first.e29362.12        first_post.o3246.1
> 14-L_Thal_first.bvars  first.e29362.13        first_post.o3826.1
> 14-L_Thal_first.vtk    first.e29362.14        first_post.o6493.1
> 14.nii.gz              first.e29362.15        first_post.o6699.1
> 14-R_Accu_first.bvars  first.e29362.16        first_post.o939.1
> 14-R_Accu_first.vtk    first.e29362.17        first_post.o9452.1
> 14-R_Amyg_first.bvars  first.e29362.2         first_post.o9547.1
> 14-R_Amyg_first.vtk    first.e29362.3         scalar.sh
> 14-R_Caud_first.bvars  first.e29362.4         scalar.sh~
> 14-R_Caud_first.vtk    first.e29362.5         slicesdir
> patze003@joy:tricam/IDEMS/analysis/miscellaneous/mesh 21% sed -n '1,3p' <
> 13-L_Accu_first.vtk >
> Missing name for redirect.
> patze003@joy:tricam/IDEMS/analysis/miscellaneous/mesh 22% sed -n '1,3p' <
> 14-L_Accu_first.vtk >
> Missing name for redirect.
> patze003@joy:tricam/IDEMS/analysis/miscellaneous/mesh 23%
> patze003@joy:tricam/IDEMS/analysis/miscellaneous/mesh 23% bash
> bash-3.00$ sed -n '1,3p' <14-L_Accu_first>
> bash: syntax error near unexpected token `newline'
> bash-3.00$ sed -n '1,3p' <14-L_Accu_first.vtk>
> bash: syntax error near unexpected token `newline'
> bash-3.00$
>
>
> *In response to your first question it is just gray, and I believe it is
> the
> surface output from the FIRST directory.  Each subject has their own
> subcortical regions as shown above.*
> *
> *
> -Edward
>
> On Wed, Oct 20, 2010 at 11:18 AM, Brian Patenaude
> <[log in to unmask]>wrote:
>
>> Hi,
>>
>> > 1.  I cannot get my 3d vtk mesh objects to show color in fslview 3d
>> > viewer.  Even with the options it won't let me.  It won't let me
>> select
>> > different mesh objects, it always says "none" and when I click
>> "surface
>> > coloured from cell data" nothing changes.
>>
>> Does the surface load, but it is just gray (is this the surface output
>> directory from FIRST? or from the shape analysis?
>>
>> In addition, what is the output of:
>>
>> sed -n '1,3p' <vtkfile>
>>
>> > 2.  Is there a way to show GLM Feat results in a vtk mesh object in
>> the
>> 3d
>> > viewer.  i.e. we have results in the amygdala and would like to create
>> a
>> > 3d mesh object from the resulting activation.  Or overlay this
>> activation
>> > in 3d on top of a vtk mesh object.
>>
>> I believe there is a function to sample the nearest non-zero voxel onto
>> a
>> surface (within a neighbourhood). Mark has this been released yet?
>>
>> Cheers,
>>
>> Brian
>>
>