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villekf / OMEGA

Open-source multi-dimensional tomographic reconstruction software (OMEGA)
https://omega-doc.readthedocs.io/en/latest/index.html
GNU General Public License v3.0
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SPECT reconstruction coding #8

Open akmal871026 opened 3 years ago

akmal871026 commented 3 years ago

Hi sir and all,

Anyone can help me to develop coding for reconstruction SPECT image?

I will pay for it. I really needed it.

Please help me.

villekf commented 2 years ago

The next release will include support for (preliminary) support for SPECT reconstruction.

akmal871026 commented 2 years ago

Dear, Sir.

May I know the estimated date?

villekf commented 2 years ago

I can't give an exact date (yet), but I'm hoping this summer (June/July).

akmal871026 commented 2 years ago

Ok, I waiting. Thank you very much sir

akmal871026 commented 1 year ago

Dear Sir,

Just to ask, any update on the SPECT reconstruction using Matlab in Github?

Thank you

On Fri, Apr 29, 2022 at 9:33 PM villekf @.***> wrote:

I can't give an exact date (yet), but I'm hoping this summer (June/July).

— Reply to this email directly, view it on GitHub https://github.com/villekf/OMEGA/issues/8#issuecomment-1113316414, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFIPQ6RHYWGEUWQ4ELSSVLVHPQI3ANCNFSM4VB4ZBSA . You are receiving this because you authored the thread.Message ID: @.***>

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MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

villekf commented 1 year ago

No update yet as there are quite a few other features that are on my priority list. A prerelease might be possible in late August, but most likely in September at the earliest.

akmal871026 commented 1 year ago

okay sir

On Mon, Jul 25, 2022 at 10:37 PM villekf @.***> wrote:

No update yet as there are quite a few other features that are on my priority list. A prerelease might be possible in late August, but most likely in September at the earliest.

— Reply to this email directly, view it on GitHub https://github.com/villekf/OMEGA/issues/8#issuecomment-1194136132, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFIPQZDU7QJKRU72U755RDVV2RDXANCNFSM4VB4ZBSA . You are receiving this because you authored the thread.Message ID: @.***>

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MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

villekf commented 1 year ago

Just as an update that I have implemented SPECT reconstruction as well. This, however, has not yet been released, but I can release a prerelease if there is need for it. The support is only for implementation 2 (meaning you need ArrayFire and OpenCL) and currently only supports OSEM.

akmal871026 commented 1 year ago

Yes, Dr. I very much need it.

But I don't know how to use OpenCL. If Matlab I can.

Can you show me the demo or video to run it?

On Mon, Sep 26, 2022, 6:32 PM villekf @.***> wrote:

Just as an update that I have implemented SPECT reconstruction as well. This, however, has not yet been released, but I can release a prerelease if there is need for it. The support is only for implementation 2 (meaning you need ArrayFire and OpenCL) and currently only supports OSEM.

— Reply to this email directly, view it on GitHub https://github.com/villekf/OMEGA/issues/8#issuecomment-1257829098, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFIPQZCMNRUZGTCHMVMLGTWAF3VTANCNFSM4VB4ZBSA . You are receiving this because you authored the thread.Message ID: @.***>

villekf commented 1 year ago

Getting implementation 2 working simply requires following the same installation steps as here.

Do you use GATE simulated SPECT data or something else? I do have a demo/example for dual-headed SPECT camera simulated in GATE.

akmal871026 commented 1 year ago

I do the simulation SPECT with SIMIND Monte Carlo.

My raw data output is attached.

On Mon, Sep 26, 2022 at 7:31 PM villekf @.***> wrote:

Getting implementation 2 working simply requires following the same installation steps as here https://github.com/villekf/OMEGA/wiki/Installation-help.

Do you use GATE simulated SPECT data or something else? I do have a demo/example for dual-headed SPECT camera simulated in GATE.

— Reply to this email directly, view it on GitHub https://github.com/villekf/OMEGA/issues/8#issuecomment-1257891268, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFIPQ5KSZTKJJWRZQZRFRTWAGCRNANCNFSM4VB4ZBSA . You are receiving this because you authored the thread.Message ID: @.***>

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MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

akmal871026 commented 1 year ago

I think the link you give is OMEGA just for PET reconstruction right?

On Mon, Sep 26, 2022 at 7:31 PM villekf @.***> wrote:

Getting implementation 2 working simply requires following the same installation steps as here https://github.com/villekf/OMEGA/wiki/Installation-help.

Do you use GATE simulated SPECT data or something else? I do have a demo/example for dual-headed SPECT camera simulated in GATE.

— Reply to this email directly, view it on GitHub https://github.com/villekf/OMEGA/issues/8#issuecomment-1257891268, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFIPQ5KSZTKJJWRZQZRFRTWAGCRNANCNFSM4VB4ZBSA . You are receiving this because you authored the thread.Message ID: @.***>

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MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

villekf commented 1 year ago

The link applies for all cases (PET, CT, and SPECT). You can already install ArrayFire and OpenCL at this point.

I've never used SIMIND, but it seems to output also Interfiles. You could try using OMEGA function loadInterfile.m to load the Interfile data. I do not have examples for SIMIND, nor can I make them, but I'd imagine the GATE example should work for SIMIND data as well, as long as you manually load the SIMIND data yourself.

The prerelease version is now available in the devel-branch: https://github.com/villekf/OMEGA/tree/devel It is, however, untested at the moment.

akmal871026 commented 1 year ago

That means the OMEGA we can get from Matlab right?

[image: omega.png]

On Mon, Sep 26, 2022 at 8:22 PM villekf @.***> wrote:

The link applies for all cases (PET, CT, and SPECT). You can already install ArrayFire and OpenCL at this point.

I've never used SIMIND, but it seems to output also Interfiles. You could try using OMEGA function loadInterfile.m to load the Interfile data. I do not have examples for SIMIND, nor can I make them, but I'd imagine the GATE example should work for SIMIND data as well, as long as you manually load the SIMIND data yourself.

The prerelease version is now available in the devel-branch: https://github.com/villekf/OMEGA/tree/devel It is, however, untested at the moment.

— Reply to this email directly, view it on GitHub https://github.com/villekf/OMEGA/issues/8#issuecomment-1257953131, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFIPQ5MW6AQ3V5R2NB4PCTWAGIRRANCNFSM4VB4ZBSA . You are receiving this because you authored the thread.Message ID: @.***>

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MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

akmal871026 commented 1 year ago

can you give the link how to install the ArrayFire and OpenCL on windows?

On Mon, Sep 26, 2022 at 8:34 PM Mohd Akmal Masud @.***> wrote:

That means the OMEGA we can get from Matlab right?

[image: omega.png]

On Mon, Sep 26, 2022 at 8:22 PM villekf @.***> wrote:

The link applies for all cases (PET, CT, and SPECT). You can already install ArrayFire and OpenCL at this point.

I've never used SIMIND, but it seems to output also Interfiles. You could try using OMEGA function loadInterfile.m to load the Interfile data. I do not have examples for SIMIND, nor can I make them, but I'd imagine the GATE example should work for SIMIND data as well, as long as you manually load the SIMIND data yourself.

The prerelease version is now available in the devel-branch: https://github.com/villekf/OMEGA/tree/devel It is, however, untested at the moment.

— Reply to this email directly, view it on GitHub https://github.com/villekf/OMEGA/issues/8#issuecomment-1257953131, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFIPQ5MW6AQ3V5R2NB4PCTWAGIRRANCNFSM4VB4ZBSA . You are receiving this because you authored the thread.Message ID: @.***>

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MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

--

___

MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

akmal871026 commented 1 year ago

this is OMEGA right?

[image: image.png]

On Mon, Sep 26, 2022 at 8:35 PM Mohd Akmal Masud @.***> wrote:

can you give the link how to install the ArrayFire and OpenCL on windows?

On Mon, Sep 26, 2022 at 8:34 PM Mohd Akmal Masud @.***> wrote:

That means the OMEGA we can get from Matlab right?

[image: omega.png]

On Mon, Sep 26, 2022 at 8:22 PM villekf @.***> wrote:

The link applies for all cases (PET, CT, and SPECT). You can already install ArrayFire and OpenCL at this point.

I've never used SIMIND, but it seems to output also Interfiles. You could try using OMEGA function loadInterfile.m to load the Interfile data. I do not have examples for SIMIND, nor can I make them, but I'd imagine the GATE example should work for SIMIND data as well, as long as you manually load the SIMIND data yourself.

The prerelease version is now available in the devel-branch: https://github.com/villekf/OMEGA/tree/devel It is, however, untested at the moment.

— Reply to this email directly, view it on GitHub https://github.com/villekf/OMEGA/issues/8#issuecomment-1257953131, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASFIPQ5MW6AQ3V5R2NB4PCTWAGIRRANCNFSM4VB4ZBSA . You are receiving this because you authored the thread.Message ID: @.***>

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MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

--

___

MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

--

___

MOHD AKMAL BIN MASUD

Pegawai Sains (Fizik),

No. 4, Jalan P7, Presint 7,

Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

H/P: +60143321631

villekf commented 1 year ago

The images are not working. The installation instructions can be found from the wiki.

akmal871026 commented 1 year ago

This is what I do in Matlab. And then?

install_mex Building with 'MinGW64 Compiler (C++)'. MEX completed successfully. Building with 'MinGW64 Compiler (C++)'. MEX completed successfully. Implementations 1 & 4 built with OpenMP (parallel) support Building with 'MinGW64 Compiler (C++)'. MEX completed successfully. Building with 'MinGW64 Compiler (C++)'. MEX completed successfully. Building with 'MinGW64 Compiler (C++)'. MEX completed successfully. LMF support enabled Building with 'MinGW64 Compiler (C++)'. MEX completed successfully. Inveon support enabled Warning: Unable to build ROOT support! If you do not need ROOT support ignore this warning. On Windows ROOT supports only 32-bit MATLAB (untested). If you are using 32-bit MATLAB make sure that ROOT was compiled with the same compiler you are using to compile this mex-file and provide the path to ROOT install folder with install_mex(0, [], [], [], 'C:/path/to/ROOT'). Compiler error is shown with install_mex(1) In install_mex (line 471) Warning: ArrayFire not found on path. Implementation 2 will not be built. Use install_mex(1, [], [], 'C:/PATH/TO/ARRAYFIRE/') to set ArrayFire path. In install_mex (line 518) Building with 'MinGW64 Compiler (C++)'. In file included from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.hpp:30:0, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\OpenCL_device_info.cpp:2: C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6029:63: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] typename std::enable_if<!std::is_pointer::value, cl_int>::type ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6456:22: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] vector* binaryStatus = NULL, ^

In file included from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.hpp:30:0, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.cpp:23: C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6029:63: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] typename std::enable_if<!std::is_pointer::value, cl_int>::type ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6456:22: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] vector* binaryStatus = NULL, ^

MEX completed successfully. Building with 'MinGW64 Compiler (C++)'. In file included from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.hpp:30:0, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\precomp.h:2, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\functions_multigpu.hpp:22, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\OpenCL_matrixfree_multi_gpu.cpp:30: C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6029:63: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] typename std::enable_if<!std::is_pointer::value, cl_int>::type ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6456:22: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] vector* binaryStatus = NULL, ^

In file included from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.hpp:30:0, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\precomp.h:2, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\functions_multigpu.hpp:22, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\multi_gpu_reconstruction.cpp:21: C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6029:63: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] typename std::enable_if<!std::is_pointer::value, cl_int>::type ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6456:22: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] vector* binaryStatus = NULL, ^

In file included from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.hpp:30:0, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\precomp.h:2, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\functions_multigpu.hpp:22, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\functions_multigpu.cpp:23: C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6029:63: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] typename std::enable_if<!std::is_pointer::value, cl_int>::type ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6456:22: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] vector* binaryStatus = NULL, ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\functions_multigpu.cpp: In function 'cl_int clGetPlatformsContext(uint32_t, float, cl::Context&, size_t&, int&, cl_uint&, cl::vector&, bool&, cl_uchar&, uint32_t, uint32_t, uint8_t)': C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\functions_multigpu.cpp:83:20: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] std::vector ignores(devices2.size()); ^

In file included from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.hpp:30:0, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.cpp:23: C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6029:63: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] typename std::enable_if<!std::is_pointer::value, cl_int>::type ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6456:22: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] vector* binaryStatus = NULL, ^

In file included from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.hpp:30:0, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\precomp.h:2, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\functions_multigpu.hpp:22, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\precomp.cpp:19: C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6029:63: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] typename std::enable_if<!std::is_pointer::value, cl_int>::type ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6456:22: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] vector* binaryStatus = NULL, ^

In file included from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.hpp:30:0, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\precomp.h:2, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\functions_multigpu.hpp:22, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\forward_backward_projections.cpp:19: C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6029:63: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] typename std::enable_if<!std::is_pointer::value, cl_int>::type ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6456:22: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] vector binaryStatus = NULL, ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\forward_backward_projections.cpp: In function 'void f_b_project(const cl_uint&, float, int, const cl::Context&, const std::vector&, size_t, const uint16_t, const float, const float, const float, const float, const mxArray, uint32_t, uint32_t, uint32_t, float, float, float, float, float, float, float, float, float, float, float, const int64_t, size_t, const uint32_t, const uint16_t, uint32_t, uint32_t, bool, uint32_t, uint32_t, uint32_t, const float, size_t, const float, size_t, const uint32_t, uint32_t, uint32_t, const uint16_t, uint8_t, size_t, uint32_t, const cl::Kernel&, const cl::Kernel&, mxArray, size_t, cl_uchar, size_t, float, float, const float, const float, const float, size_t, size_t, size_t, bool, int32_t, uint32_t, uint16_t, uint16_t, float, const mxArray, bool, bool, float, float, float, float, const float, size_t, uint8_t, size_t, const mxArray, uint32_t, bool, int64_t, float, const float, int64_t)': C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\forward_backward_projections.cpp:792:22: warning: ignoring attributes on template argument 'cl_ulong {aka long long unsigned int}' [-Wignored-attributes] std::vector globals(num_devices_context, 0ULL); ^

In file included from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\opencl_error.hpp:30:0, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\precomp.h:2, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\functions_multigpu.hpp:22, from C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\multigpu_OSEM.cpp:19: C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6029:63: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] typename std::enable_if<!std::is_pointer::value, cl_int>::type ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\cl2.hpp:6456:22: warning: ignoring attributes on template argument 'cl_int {aka int}' [-Wignored-attributes] vector binaryStatus = NULL, ^ C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\multigpu_OSEM.cpp: In function 'void OSEM_MLEM(const cl_uint&, float, int, const cl::Context&, const std::vector&, size_t, const uint16_t, const float, const float, const float, const mxArray, const mxArray, uint32_t, uint32_t, uint32_t, uint32_t, const mxArray, float, float, float, float, float, float, float, float, float, float, float, const int64_t, size_t, const uint32_t, const uint16_t, uint32_t, uint32_t, bool, uint32_t, uint32_t, uint32_t, const float, size_t, const float, size_t, uint32_t, float, uint32_t, const uint32_t, uint32_t, uint32_t, const uint16_t, uint8_t, size_t, uint32_t, const cl::Kernel&, const cl::Kernel&, const cl::Kernel&, const cl::Kernel&, const cl::Kernel&, const cl::Kernel&, const cl::Kernel&, size_t, float, float, const float, const float, const float, size_t, size_t, size_t, bool, bool, cl_uchar, bool, int32_t, uint32_t, uint16_t, uint16_t, float, mxArray, bool, float, float, float, float, const float, size_t, size_t, bool, const float, size_t, uint32_t, bool, int64_t, float, const float, int64_t, cl::vector)': C:\Users\Akmal\AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\OMEGA - Open-source MATLAB emission tomography software\source\multigpu_OSEM.cpp:109:22: warning: ignoring attributes on template argument 'cl_ulong {aka long long unsigned int}' [-Wignored-attributes] std::vector cumsum((num_devices_context + 1u) * subsets, 0); ^

MEX completed successfully. Implementation 3 built

On Mon, Sep 26, 2022 at 9:16 PM villekf @.***> wrote:

The images are not working. The installation instructions can be found from the wiki https://github.com/villekf/OMEGA/wiki/Installation-help#opencl.

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villekf commented 1 year ago

You need Visual Studio or then you need to manually build ArrayFire MinGW. See the same wiki page for details if you want to manually build ArrayFire with MinGW, but I highly recommend installing and using Visual Studio instead.

Furthermore, you need to use the devel-branch to get SPECT support. You seem to have used the MATLAB toolbox from releases.

akmal871026 commented 1 year ago

I download OMEGA-devel. I also install Visual Studio. Then how to run? Do you have any manuals?

[image: image.png]

On Mon, Sep 26, 2022 at 9:29 PM villekf @.***> wrote:

You need Visual Studio or then you need to manually build ArrayFire MinGW. See the same wiki page for details if you want to manually build ArrayFire with MinGW, but I highly recommend installing and using Visual Studio instead.

Furthermore, you need to use the devel-branch https://github.com/villekf/OMEGA/archive/refs/heads/devel.zip to get SPECT support. You seem to have used the MATLAB toolbox from releases.

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akmal871026 commented 1 year ago

This is what I tried for PET.

How about SPECT?

>> main_PET

Using implementation 4. OSEM reconstruction method selected. No precomputed data will be used. Improved Siddon's algorithm used with 1 transaxial ray and 1 axial ray. Using STATIC sinogram data (prompts). Every 8th column measurement is taken per subset. Using an image (matrix) size of 128x128x63 with 4 iterations and 8 subsets. Preparing for reconstruction Warning: Variable 'appliedCorrections' not found.

In loadStructFromFile (line 2) In reconstructions_main (line 299) In main_PET (line 1599) Starting image reconstruction OSEM sub-iteration 1 took 8.1746 seconds OSEM sub-iteration 2 took 7.4217 seconds OSEM sub-iteration 3 took 7.2445 seconds OSEM sub-iteration 4 took 7.6869 seconds OSEM sub-iteration 5 took 7.5651 seconds OSEM sub-iteration 6 took 7.3848 seconds OSEM sub-iteration 7 took 8.6126 seconds OSEM sub-iteration 8 took 7.6928 seconds OSEM iteration 1 took 61.8657 seconds OSEM sub-iteration 1 took 2.5157 seconds OSEM sub-iteration 2 took 2.5123 seconds OSEM sub-iteration 3 took 2.4685 seconds OSEM sub-iteration 4 took 2.5039 seconds OSEM sub-iteration 5 took 2.6661 seconds OSEM sub-iteration 6 took 2.7013 seconds OSEM sub-iteration 7 took 2.4208 seconds OSEM sub-iteration 8 took 2.4233 seconds OSEM iteration 2 took 20.2469 seconds OSEM sub-iteration 1 took 2.4376 seconds OSEM sub-iteration 2 took 2.3936 seconds OSEM sub-iteration 3 took 2.4203 seconds OSEM sub-iteration 4 took 2.4735 seconds OSEM sub-iteration 5 took 2.5815 seconds OSEM sub-iteration 6 took 2.6481 seconds OSEM sub-iteration 7 took 2.4135 seconds OSEM sub-iteration 8 took 2.3821 seconds OSEM iteration 3 took 19.7845 seconds OSEM sub-iteration 1 took 2.3823 seconds OSEM sub-iteration 2 took 2.3897 seconds OSEM sub-iteration 3 took 2.3407 seconds OSEM sub-iteration 4 took 2.3844 seconds OSEM sub-iteration 5 took 2.4194 seconds OSEM sub-iteration 6 took 2.4179 seconds OSEM sub-iteration 7 took 2.4637 seconds OSEM sub-iteration 8 took 2.341 seconds OSEM iteration 4 took 19.1721 seconds Reconstruction process took 123.7533 seconds

On Mon, Sep 26, 2022 at 9:58 PM Mohd Akmal Masud @.***> wrote:

I download OMEGA-devel. I also install Visual Studio. Then how to run? Do you have any manuals?

[image: image.png]

On Mon, Sep 26, 2022 at 9:29 PM villekf @.***> wrote:

You need Visual Studio or then you need to manually build ArrayFire MinGW. See the same wiki page for details if you want to manually build ArrayFire with MinGW, but I highly recommend installing and using Visual Studio instead.

Furthermore, you need to use the devel-branch https://github.com/villekf/OMEGA/archive/refs/heads/devel.zip to get SPECT support. You seem to have used the MATLAB toolbox from releases.

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Institut Kanser Negara,

62250 Putrajaya.

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Jabatan Perubatan Nuklear,

Institut Kanser Negara,

62250 Putrajaya.

E-mail: @.***

        ***@***.***

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villekf commented 1 year ago

The wiki is the manual.

For SPECT, use gate_SPECT_main.m and modify it to work with your SIMIND data. There is no specific documentation for SPECT yet as this is still an unofficial release.

akmal871026 commented 1 year ago

Sir, I just play sound using PET sinogram data. using this command: >>main_PET

Then, the result is attached.

then which one of the images?

pz? Cylindrical_PET_example_cylpet_example_sinogram... https://drive.google.com/file/d/1uKKMhO2gvKGe3WmpFuquUFQS44wPJSR1/view?usp=drive_web PET.mat https://drive.google.com/file/d/1AkIBCTM-8pNaSCvcGu1Ig7hLofpRE6r7/view?usp=drive_web

On Mon, Sep 26, 2022 at 10:06 PM villekf @.***> wrote:

The wiki https://github.com/villekf/OMEGA/wiki is the manual.

For SPECT, use gate_SPECT_main.m and modify it to work with your SIMIND data. There is no specific documentation for SPECT yet as this is still an unofficial release.

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villekf commented 1 year ago

pz indeed contains the output images. You can use visualize_pet.m to visualize it or you can do it manually. The same visualization can be used for SPECT and CT data as well.

akmal871026 commented 1 year ago

ok Dr...thank you very much....

On Tue, Sep 27, 2022 at 4:36 PM villekf @.***> wrote:

pz indeed contains the output images. You can use visualize_pet.m to visualize it or you can do it manually. The same visualization can be used for SPECT and CT data as well.

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akmal871026 commented 1 year ago

Dr, could you help me to make it my output (as attached) simulation so that can synchronize in gate_main_SPECT.m

I don't know which output is the real output matching in your algorithm.

Please Dr, begging you to help me.

On Tue, Sep 27, 2022 at 4:36 PM villekf @.***> wrote:

pz indeed contains the output images. You can use visualize_pet.m to visualize it or you can do it manually. The same visualization can be used for SPECT and CT data as well.

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villekf commented 1 year ago

I don't quite understand what you are asking, but you'll find the output in the pz-cell matrix. The first non-empty cell contains the output reconstruction in the case of SPECT.

If you are asking me to modify gate_main_SPECT.m to match your data, I don't know how to do that. As I said, I have no experience with SIMIND. If that is an issue, you could consider migrating to GATE.