CODEWITHSUNDEEP
matlabwireframenifti
Green_Crim
Green_Crim

Reputation: 1

Creating a 3D wireframe cortical model from MNI brain template with Matlab using MyRobustCrust

I am attempting to create a wireframe 3d model from an MNI brain template using MyRobustCrust on matlab. My goal is to be able to determine MNI coordinates on the cortical surface.

To do this, I'm following the instructions listed at this site: http://soundsfromthenorth.com/?p=3

Unfortunately, the admin doesn't seem to be active any more.

Following the site's instructions, I have successfully extracted the data set ("MNI152_T1_2mm_brain_mask.nii") from FSL. However, when I go to run MyRobustCrust, using the following input (as directed by the site), I get a blank graph.

Code input

>> [t,tnorm]=MyRobustCrust(p);
figure(1)
hold on
axis equal
h=trisurf(t,p(:,1),p(:,2),p(:,3),'facealpha',0.4,...
...'facecolor',[1 1 1],'edgecolor',[0.8 0.8 0.8]);
view(3);
axis vis3d

Code output: 

Added Shield: 0.0559 s
Delaunay Triangulation Time: 0.6515 s
Connectivity Time: 0.0796 s
Circumcenters Time: 0.0168 s
Warning: Brute continuation necessary 
> In MyRobustCrust>Marking (line 380)
  In MyRobustCrust (line 106) 
Warning: 1000 th level was reached\n 
> In MyRobustCrust>Marking (line 412)
  In MyRobustCrust (line 106) 
99.9941 % of Tetraedroms were checked
Walking Time: 0.2084 s
Manifold extraction Time: 0.3782 s
Total Time: 1.4809 s
 view(3);
        |
Error: Unbalanced or unexpected parenthesis or bracket.

I'm unfortunately very new to neuroimaging and to Matlab. Does anyone have any suggestions as to what I may be doing wrong here? Does the error signal indicate an unbalance or unexpected parenthesis in the code for MyRobustCrust or in the data?

Upvotes: 0

Views: 493

Answers (1)

Setsu
Setsu

Reputation: 1218

I hope I understand you correctly, but it seems to me that you're trying to take transverse-plane (axial-plane) markings into MNI coordinates.

If so, then perhaps you should try xjView (note: requires SPM). This is a graphical interface that is mainly used for overlaying contrasts over a template, among a tone of other features (creating masks, generating stats tables ...etc). In your case, you can simply load the default MNI image (avg152T1 or T2 from SPM) and click around the 3-axis views on the top right; the MNI coordinates will be on the bottom left.

enter image description here

Upvotes: 1

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