[Homer-users] Error in using create_HeadVox.m

[Maheen Siddiqui]

Hi Jay, 

Sorry for being unclear in my previous email; the script is available to download from the Homer2 webpage (more details here: http://homer-fnirs.org/faq/#subjectspecificanatomy under subject specific anatomy). 

The script creates all the files needed to import subject anatomy into Atlas Viewer GUI and just requires a pial surface mesh file and a head surface mesh file. 

And yes I am trying to convert freesurfer files to use in Atlas Viewer. I did the recon-all on a T1 weighted MRI scan so I have all the segmented files as well as surface files but they are separated into right and left hemispheres. 

I would appreciate any advice you could provide! 

Thanks 

Maheen 


> On 10 Feb 2016, at 18:20, jdubb at nmr.mgh.harvard.edu wrote:
> 
> 
> 
> Hi Maheen,
> I'm not clear about this issue.
> 
> I couldn't find a script called create_HeadVox.m
> under Homer2. Where is this script supposed to be in the
> Homer2 folder structure?
> 
> Are you trying to convert Freesurfer files to AtlasViewer?
> If so I'll need more info on what Freesurfer files you have
> in your subject folder.
> 
> Jay
> 
> 
> 
>> Dear Homer Users,
>> 
>> I am trying to use the "create_HeadVox.m" script under Homer to create the
>> necessary files to have an individual subject anatomy in Homer. However, I
>> keep getting the following error message and I'm unsure why.
>> 
>> *Error using patch*
>> *Faces values must be >= 1.0*
>> 
>> *Error in trisurf (line 93)*
>> *h = patch('faces',trids,'vertices',[x(:) y(:)
>> z(:)],'facevertexcdata',c(:),...*
>> 
>> *Error in create_HeadVox (line 56)*
>> *h=trisurf(fa,va(:,1),va(:,2),va(:,3),va(:,1));*
>> 
>> I used the "write_surf.m" script to create the meshes in the following way:
>> 
>> *write_surf('pialsurf.mesh',pialn,pialf);*
>> 
>> where pialn are the nodes of the pial surface and pialf are the faces of
>> the pial surface. Prior to this I had to use the "mergemesh" function in
>> iso2mesh to combine the left handside and right handside individual
>> surfaces that FreeSurfer creates.
>> 
>> If anyone could tell me where I am going wrong I would be very grateful!
>> 
>> Thanks,
>> 
>> Maheen
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> 
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