NITRC SPHARM-MAT Forum: help

problem with surface orgin

Giulia Baldassari — Wed, 01 Jun 2022 10:24:47 GMT

Dear all,
I am a researcher of Bambino Gesù hospital in Rome. I am having problems extracting the surface of the hippocampus and the respective cornus ammonis because when I obtain the vtk surface of cornus ammois this doesn't respect the original position on the Hippocampus but is centered in another origin.

-image1: green cornus ammonis and red hippocampus reconstructed with Spharm-Mat and visualized in 3D Slicer;
-image2: green cornus ammonis and blue hippocampus reconstructed directly in 3D Slicer.
As you can see in image 1, the cornus ammonis doesn't occupy the right position, which instead can be seen in image 2.
How can I maintain the correct position of the cornus ammonis with respect to the hippocampus?
Thanks,
Giulia.

inHouse Topology_fix

Rizwan Khan — Sat, 28 Sep 2019 7:09:06 GMT

Dear all,

I am fixing the topology of my #D binary image so that to remove any bad voxels. I am getting the following error.

Error:

InHouse_Fix
Make a simply connected volume by removing bad voxels
(1) outlier or hole, (2) vertex conn., (3) edge conn., (4) ring or hole, (5) s(1) single ring, (2)
Index in position 1 exceeds array bounds.

Error in gen_surf_data (line 121)
vertices = vertices.*vxsize(ones(1,size(vertices,1)),:);
Error in fix_bad_topology (line 91)
[vertices, faces] = gen_surf_data(roi,origin,vxsize);
Error in SpharmMatUtilTopologyFix (line 46)
[bim_new,origin_new,vxsize_new,outNames{end+1}] = fix_bad_topology(file, confs);
Error in SPHARM_MAT>RunTag_Callback (line 659)
SpharmMatUtilTopologyFix(handles.userdata.InHouse_Fix, handles.userdata.inObjs, 'InHouse_Fix');
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in SPHARM_MAT (line 70)
gui_mainfcn(gui_State, varargin{:});
Error while evaluating UIControl Callback.

Please help me out to fix this issue.

thanks

Rizwan

RE: Bigger sizes of micro-CT images

Shan Cong — Wed, 25 Sep 2019 14:06:39 GMT

[i]Originally posted by Rizwan Khan:[/i][quote]Dear all,

I am working on 3D binary images of micro-CT of sand particles. Size is approx. of 7MB of one image. I am not able to see image after topology fix .

Error says: Image cannot be displayed

Please help me out to solve this issue whether I can use this software for the analysis such large sizes images.

thanks

Rizwan[/quote]
[color=#000000]You should extract your region of interest first instead of using the whole image. [/color]

Bigger sizes of micro-CT images

Rizwan Khan — Wed, 25 Sep 2019 13:37:49 GMT

Dear all,

I am working on 3D binary images of micro-CT of sand particles. Size is approx. of 7MB of one image. I am not able to see image after topology fix .

Error says: Image cannot be displayed

Please help me out to solve this issue whether I can use this software for the analysis such large sizes images.

thanks

Rizwan

INSTALLATION OF SPHARM-MAT

Rizwan Khan — Fri, 20 Sep 2019 5:33:32 GMT

Good Morning all,

I am planning to use this tool for the reconstruction of surfaces of micro-CT images of sand particles.

I am following the documentation available on the website but can't install

Since I am new and comes from civil engineering background, I humbly request you to help me in installing this nice tool.

Currently, I am a Dell workstation with windows 10 and Matlab 2019a version.

thanks

Rizwan

SPHARM_PDM matlab

mraiola — Tue, 14 May 2019 21:01:48 GMT

Goodmorning,

I'm using SPHARM for the first time to parametrize a voxel Heart surface. I want to run SPHARM PDM on Matlab 2018b by using Windows 10.

Is there any person who is using SPHARM PDM on Matlab ? I'm following this tutorial (http://www.iu.edu/~spharm/)

Thank you in advance,

Morena

RE: error in initParamCALD

Karol Dawidowicz — Mon, 08 Oct 2018 6:32:04 GMT

I found a solution
instead "file" should be "filename"

error in initParamCALD

Karol Dawidowicz — Wed, 19 Sep 2018 9:56:11 GMT

Hi,
I have some troubles with the parameterization step. I tried to go trough Exercise 3.1 (the example data) but
I have the following message in Matlab (2014a):

Undefined function or variable 'file'.
Error in initParamCALD (line 43)
[path, name, ext] = fileparts(file);
Error in SpharmMatParamTriaMesh (line 52)
[sph_verts, name3] = initParamCALD(vertices, faces, name2, confs);
Error in SpharmMatParameterization (line 49)
[vertices_new, faces_new, sph_verts_new, outNames{end+1}] = SpharmMatParamTriaMesh(file, confs);
Error in SPHARM_MAT>RunTag_Callback (line 601)
SpharmMatParameterization(handles.userdata.ParamCALD, handles.userdata.inObjs, 'ParamCALD');
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in SPHARM_MAT (line 70)
gui_mainfcn(gui_State, varargin{:});
Error while evaluating uicontrol Callback

I would appreciate any help,
Thanks

RE: Average Objects using SPHARM MAT

dongji han — Thu, 23 Aug 2018 11:31:55 GMT

Hello! I have the same problem with you.It is a trouble.Can you give me some suggestions? Thank you very much if you reply me.

Average Objects using SPHARM MAT

C. Srinidhi Ragunathan — Mon, 16 Oct 2017 9:20:44 GMT

I am currently using the SPHARM-MAT toolbox for calculating the average of a set of points clouds, and then using it further to create a shape model.
The output of the Average Object is 'fvec' or the coefficients of the spherical harmonics.
I would like to know if simple linear algebra (multiplying the Spharm Basis function with 'fvec') will result in the coordinates of the point cloud in the cartesian space.
Do I need to align the spherical vertices of all my training point clouds, to obtain the mean shape of the same ? And then use this mean spherical vertices to calculate the cartesian coordinates ?