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Surfaces in Papaya

Questions or comments about Mango, webMango, iMango or Papaya.

Moderator: Michael Martinez

Surfaces in Papaya

Postby Joel » Mon Jun 20, 2016 7:49 pm

In Papaya, I am trying to load a Freesurfer surface onto the T1-weighted MRI (in Nifti) that I used to generate it. I got the surface into Gifti format by running Freesurfer mris_convert lh.pial lh.pial.gii

The javascript console says "Uncaught Error: Surface is missing normals information!"

What might I be doing wrong?

Thanks,
Joel
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Re: Surfaces in Papaya

Postby Michael Martinez » Tue Jun 21, 2016 11:48 am

Papaya definitely needs the normals to render the surface. I'm guessing the original file (lh.pial) didn't contain normals either.

Technically, normals can be calculated in the software, but more often they are included in the surface file to save the software from the extra work. Papaya currently is in that group and expects that the normals are in the file.

One thing you can do is take the lh.pial.gii file you have and open it in Mango. (You'll have to first load the associated NIFTI file.) Mango does generate normals if they aren't in the file. Then export again from Mango as GIFTI, which should then include normals which Papaya can then read.

I'll also add a feature request to fix Papaya so that it can handle generating normals itself.
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Re: Surfaces in Papaya

Postby Michael Martinez » Tue Jun 21, 2016 11:49 am

P.S. Another thing you can try is to see if there is some option to tell the software to include normals when it writes the surface file.
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Re: Surfaces in Papaya

Postby Michael Martinez » Tue Jun 21, 2016 5:18 pm

The latest build of Papaya now supports GIFTI surfaces files without normals data.
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Re: Surfaces in Papaya

Postby Joel » Wed Jun 22, 2016 11:50 pm

Wow, that was fast. Thank you so much.

It works and looks great!
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Re: Surfaces in Papaya

Postby yozdemir » Mon Sep 11, 2017 3:08 pm

Hi,

I am trying to open up gifti images in the latest build of Papaya but the system tells me the gifti lacks "triangle information." Do you know what this means? The gifti were created both in Freesurfer and Brainvoyager (gifti plu gin). Is there a way to visualize these gifti files in Mango? Because if that is the case I will prefer Mango.

Best,
Idil
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Re: Surfaces in Papaya

Postby admin » Sat Sep 16, 2017 8:22 pm

The "triangle information" is one part of the data it needs to read in order to display the surface. If there is a way for you to share the surface file with me, I can take a look. In general, both Mango and Papaya support GIFTI .surf files.
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