vistalab / vistasoft

VISTASOFT is the main software repository of the VISTA lab at Stanford University.
http://vistalab.stanford.edu
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Unable to process sample data #281

Closed neurolabusc closed 6 years ago

neurolabusc commented 6 years ago

The Vista Lab Mesh web page includes a sample dataset for creating a mesh. The tutorial includes a download with 'right.Class' and 'left.Class' files and the tutorial suggests we can process one of these files with the msh = meshBuildFromClass(fName); function. However, the function crashes with the sample datasets. Looking at meshBuildFromClass code it appears to expect either a Matlab structure or a NIfTI image. Is this .Class format obsolete? Is there some function to load this .Class format as a Matlab structure, or a function to convert the .Class file to NIfTI?

JWinawer commented 6 years ago

Hi Chris,

The .Class format is generally out of date, though it is possible that it will still work with some functions. We use either nifti files to generate meshes, or we import meshes directly from Freesurfer. For the latter, see these tutorials (esp the first two under the header, 'Volume anatomy, classification file, and meshes'):

https://github.com/vistalab/vistasoft/wiki/Ernie-Tutorials

Jon

On Sun, Mar 4, 2018 at 2:43 PM, Chris Rorden notifications@github.com wrote:

The Vista Lab Mesh web page includes a sample dataset for creating a mesh https://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/Mesh#mrVista_meshes. The tutorial includes a download with 'right.Class' and 'left.Class' files and the tutorial suggests we can process one of these files with the msh = meshBuildFromClass(fName); function. However, the function crashes with the sample datasets. Looking at meshBuildFromClass code it appears to expect either a Matlab structure or a NIfTI image. Is this .Class format obsolete? Is there some function to load this .Class format as a Matlab structure, or a function to convert the .Class file to NIfTI?

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-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/

neurolabusc commented 6 years ago

Jon- Great. Can I suggest updating or deleting the older web page?

-chris

JWinawer commented 6 years ago

Yes, we should, and will. But unfortunately, it will take a bit of time.

In the meantime, I suggest sticking to the wiki on the GitHub page rather than the Stanford web page. There was a plan to merge them but this has been slowed down by limited time, people, and money.

On Mon, Mar 5, 2018 at 8:19 AM, Chris Rorden notifications@github.com wrote:

Jon- Great. Can I suggest updating or deleting the older web page https://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/Mesh#mrVista_meshes ?

-chris

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/281#issuecomment-370416169, or mute the thread https://github.com/notifications/unsubscribe-auth/ACBX3mLTe7Rz3CnrgBhcFkatfERxB0mOks5tbTtXgaJpZM4Sbd6J .

-- Jonathan Winawer Assistant Professor of Psychology and Neural Science

New York University 6 Washington Place New York, NY, 10003 (212) 998-7922 (phone) (212) 995-4018 (fax) jonathan.winawer@nyu.edu http://psych.nyu.edu/winawer/