Search found 9 matches

by kathleenACE
Thu Apr 19, 2012 7:03 pm
Forum: Anatomist
Topic: question overlap meshes
Replies: 7
Views: 8288

Re: question overlap meshes

Yes FreeSurfer does resample data and some other steps that are a mystery to me. It seems to resize and reshape the brain somehow - I believe they have called this process "unwarping". My initial attempts were to just take the freesurfer data back into native space before importing it but ...
by kathleenACE
Tue Apr 17, 2012 11:48 pm
Forum: BrainVISA
Topic: aparc 2 BrainVisa
Replies: 8
Views: 3206

Re: aparc 2 BrainVisa

I just figured out how to do this. See my reply to your other post:

viewtopic.php?f=6&t=1622&p=5987#p5987

Let me know if you run into any problems or need clarification.
-Kathleen
by kathleenACE
Tue Apr 17, 2012 11:47 pm
Forum: Anatomist
Topic: question overlap meshes
Replies: 7
Views: 8288

Re: question overlap meshes

Hi users, I just figured out how to get the aparc onto the mesh as well. I transformed the spherereg and the standard ico meshes into the brainvisa space using the transform from the inverted registration mentioned above. Then I ran "06 Computation of resampling parameters". Then I took th...
by kathleenACE
Tue Apr 17, 2012 8:05 pm
Forum: Anatomist
Topic: question overlap meshes
Replies: 7
Views: 8288

Re: question overlap meshes

yes! I solved it by registering their actual T1 volumes to each other, then I used AimsMeshTransform to apply that transformation to the mesh. For my purposes, I decided to register my T1 to the freesurfer T1 (001.nii) in FSL using FLIRT, convert the .mat file to .trm (in brainvisa), invert the tran...
by kathleenACE
Fri Jan 07, 2011 8:07 pm
Forum: BrainVISA
Topic: Freesurfer in BrainVISA
Replies: 1
Views: 1474

Freesurfer in BrainVISA

Does anyone know where I can get this freesurfer toolbox for BrainVISA?
http://www.brainvisa.info/doc/brainvisa ... eline.html
by kathleenACE
Thu Sep 10, 2009 10:06 pm
Forum: AIMS
Topic: Mesh commands
Replies: 9
Views: 8909

Re: Mesh commands

good. I did subtract the skeleton out in the mesh posted below. sounds like you agree that this is an acceptable method for improving the mesh. I think I will stick with the result of AimsMeshWhite without smoothing, as I don't want to lose any voxels for my cortical thickness and surface area measu...
by kathleenACE
Mon Aug 31, 2009 9:29 pm
Forum: AIMS
Topic: Mesh commands
Replies: 9
Views: 8909

Re: Mesh commands

I prefer not to use AimsMeshBrain with VipOpenFold as it seems to miss the outer pial edge of the brain on my subjects. The attached images are (1) the brain mask and sucal map; (2) the mesh from the pipeline overlaid on the mask, (3) the mesh that I made from AimsMeshWhite overlaid on the mask. The...
by kathleenACE
Fri Jul 31, 2009 11:24 pm
Forum: AIMS
Topic: Mesh commands
Replies: 9
Views: 8909

Mesh commands

Dear BrainVisa experts, I have been making meshes from brain masks using the AimsMeshBrain command. I recently tried the AimsMeshWhite command and found that the results looked better. Can you tell me how these algorithms work and/or what is the difference between them? Is it appropriate to use Aims...
by kathleenACE
Mon May 25, 2009 8:07 pm
Forum: BrainVISA
Topic: display Cortical Surface Parameterization on gyrus mesh
Replies: 3
Views: 1920

Re: display Cortical Surface Parameterization on gyrus mesh

You can project the result of the white matter parcellation onto the hemimesh with a fusion: 1. make the fusion of the .tex and white matter mesh as you would to view it 2. select that fusion and the hemimesh and make another fusion, but change the type of fusion to interpoler 3. view the interpoler...

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