didsr / victre Goto Github PK

Hello Team VICTRE,

Thank you for developing this great software and for making it open source.
In your documentation, you give the instruction to install this software on the Ubuntu 16.04 system. But I am using Centos 7 system, could you give me some advice to intall breastPhantom based on Centos 7.
Thank you very much.

Best wishes,
Li Yang

Hi Thanks for sharing a good dataset and pipeline codes

I am inquiring because there is confusion in viewing the data.
It is different from the DM projection image introduced by the article and the DM projection image uploaded on VICTRE.
Changing brightness and contrast makes it difficult to obtain similar images.

How do I get an article image from the VICTRE data?

1. VICTRE image

2. Article image

Dear team VICTRE,

Thank you for providing this excellent open source code of Breast Phantom. I have been working on the breast Phantom and could execute with required parameters smoothly.

1. I would like to extract individual parameters from the Phantom. i.e. How can I extract only "Duct" from the Phantom? Or any other components.
2. How can I scale down the model so that the tissue components can be integrated into another model.?

Thanks and Regards,

Sunag R A.

Dear authors,
first of all thanks for the precious work.

I would like to ask you help because I am having a problem when installing the breastPhantom on my UBUNTU 16.04 machine.

I am able to build all the libraries (libduct.a, libcreateArtery.a etc..) but Im encountering an error in linking CXX executable breastPhantom.

I attach a screenshot.

Thank you for the assistance.

Best regards,
Bruno De Santi

Hello, Thank you for sharing this interesting project!

I have installed the VICTRE pipeline using Ubuntu 16.04 and worked well.

But It doesn't work out in a new environment( Ubuntu 20.04, NVIDIA RTX 3090, Cuda 11.2, CuDNN 8.1.0).
Can I possibly get some help with this?

1. How should I modify the vtk version in BreastPhantom and BreastCompress? Is vtk6 not available in Ubuntu 20.04?

2. In X-ray imaging, the following error appeared.

MC-GPU_v1.5b.cu: In function ‘int main(int, char**)’:
MC-GPU_v1.5b.cu:1169:33: warning: ‘%04d’ directive writing between 4 and 10 bytes into a region of size between 3 and 252 [-Wformat-overflow=]
1169 | sprintf(file_name_output_num_p, "%s_%04d", file_name_output, num_p); // Create the output file name with the input name + projection number (4 digits, padding with 0)
| ^~~~~~~~~
MC-GPU_v1.5b.cu:1169:33: note: directive argument in the range [0, 2147483646]
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:31: note: ‘__builtin___sprintf_chk’ output between 6 and 261 bytes into a destination of size 253
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

could you give me some advice or any help?

Thanks & Regards,
Ahyeong Lee

Hello Team VICTRE,

First, thank you for developing this great project and for making it open source. I am having an issue with the installation of the breastCompress step, the operative system I use is Ubuntu 20.04.

I have already installed the breastPhantom component and it works correctly, I had to modify the instructions a little since I used VTK version 9.0.1. I add this information in case it is relevant.

The issue I am facing right now consists on the next: after an apparent successful installation of the breastCompress step, I try to run it from the terminal but I get the next:

Total bytes read = 2593976940
Segmentation fault (core dumped)

The installation was made as follows:

First, in a terminal window I ran the commands in section 2.3 of the documentation, but I skipped those that I had already ran for the installation of breastPhantom, this is, I skipped the first 3 lines (cmake vtk6 libvtk6-dev \libblas-dev liblapack-dev \libboost-dev libboost-program-options-dev) and proceeded from the fourth line and the rest of the section.

When I was setingt up FEBio, I installed the latest version (FEBio 3.1, Nov 23, 2020), and I see, in the documentation of breastCompress, that the software expects the executable to be in "PATH/bin/febio2.lnx64", however, in the bin folder of FEBio there is no such a file, instead there is an executable file named febio3. The other available FEBio versions in their webpage are all from 2020. I do not know if this version disagreement is what is causing the issue.

I am very thankful for any help I can get to overcome this issue. And again, thanks for making this amazing project available.

Kind regards.

Nicole H.

Hi!

Thank you so much for this very interesting project!

I'm having issues when it comes to running the reconstruction code(the binary crashes) on the breast models you have provided and so I can't produce images.

In order for you to understand exactly what's going on, I've added a detailed description of the steps I've taken in the following gist:
a detailed description

Hello!

I have a few (related) questions about the ROI coordinates for the dataset. I'm afraid I may be missing a critical bit of information and would be very grateful for your help. I'm having some issues reconciling the ROI data from the Github repo (https://github.com/DIDSR/VICTRE_DM_ROIs) and the dataset provided on The Cancer Imaging Archive. Specifically, my goal is to obtain the voxel coordinates of signal-positive ROIs.

1. The ROIs saved in the VICTRE_DM_ROI repo are split between "signal-absent" and "signal-present" ROIs. However, the "signal-present" ROIs only have pixel coordinates for the mammograms but not voxel coordinates for the reconstructed volumes. Is there a way to locate the ROIs in the DBT volumes themselves?
2. Related to that, I'm a bit confused about the the "signal-absent" ROIs. The readme.txt files state that the ROIs are given in voxel coordinates, but shouldn't that mean the Z-coordinate shouldn't be greater than the number of slices generated by the reconstruction? I'm seeing far larger Z-values, e.g. the file roi_SA_2000680575.loc has the coordinates:

300 1346 159 184 1272
985 1291 498 622 1301
409 1177 646 261 1371
634 1184 178 390 1371
360 729 312 224 1653
1029 1160 451 647 1384
663 1163 492 418 1381
754 907 599 480 1544
568 1417 203 350 1227
898 1187 577 571 1365
471 1262 204 290 1323
378 1611 277 234 1105

In addition, the x- and y- coordinates (first two columns?) appear to be greater than the actual dimensions of the corresponding volume slices.

I feel like I'm missing a critical detail. How can I obtain the locations of masses and calcifications in the reconstructed DBT volumes?

Thank you so much for your help!

Logo

First, thanks for releasing this super interesting source code!

It is currently not possible to run the x-ray imaging step due to several missing material files, for example:
glandular__5-120keV.mcgpu
CalciumOxalate__5-120keV.mcgpu
W__5-120keV.mcgpu
Se__5-120keV.mcgpu

and also other material files.

Note - following this example:
https://github.com/DIDSR/VICTRE_MCGPU/blob/master/MC-GPU_v1.5b_sample_mammo_and_DBT_simulation.in

Hello, thank you for making available this interesting and useful tool.

I have a question about the generation of some phantoms. Each phantoms is identified by its seed, however, sometimes the seed is preceded by a "-" (I guess we could say that some phantoms have negative seeds). I have noticed that including the "-" with the rest of the seed is necessary to use that phantom on the rest of the VICTRE pipeline.

I am curios about this "-", does it affect the treatment of that phantom on the rest of the VICTRE pipeline? Does it indicate something?

Hello Team VICTRE,

Thank you for developing this wonderful software, and I have recently tried to generate some phantoms of breast. Therefore, I found the format of lesionInsert.py is very confusing. For example, I am not sure that which “if” is corresponding to the “elseif” without alignment. I will appreciate it if you can give a clear guide.

Best regards!
zmm

Hello. I have been using the VICTRE pipeline (specifically breastPhantom, breastCompress, breastCrop and x-ray imaging) and recently noticed that two images (mammography) that I got from different phantoms that I generated, with different fat percentage, look very similar.

I took the following steps:

1. I used breastPhantom to generate a handful of phantoms with different fat percentage. I used the file 'breastPhantom/cfg/VICTRE_dense.cfg' and only changed line 25, target fat.
2. I used breasCompress and breastCrop normally.
3. I generated .in files for the x-ray imaging part of the pipeline. Here, I edited the file 'VICTRE_MCGPU/example_simulations/MC-GPU_v1.5b_hetero_phantom_mammo_fast.in', specifically lines:
   -22, I changed the number of stories to the original number 1.7e11
   -39, output image filename
   -68, 69, 70 and 75 to match the cropped phantoms size
   -73, voxel geometry file
4. I used the modified files and the instructions in 'VICTRE_MCGPU/example_simulations/readme.md' to generate simulated mammography images.

Now, I am looking at a couple of the files using ImageJ and they look very similar. When I modify the brightness I see differences on the internal structures of the images, but why do the shape of the breast looks the same? I am interested in generating a small synthetic dataset of images and I would like to be able to generate various shapes and sizes of breast, how can I do so?

I attach the image with the shape that I am getting repeatedly (no brightness modification)

along with some of the images with the brightness modified where I do see they are from different phantoms

Thanks in advance for any help!

Dear authors,

first of all thanks for the precious work.I am an undergraduate student.

I would like to ask you help because I am having a problem when installing the breastPhantom on my UBUNTU 16.04 machine.l have successfully completed the previous part,but in the process of lesion insertion, the Python code always fails to run successtuly, and it still fails to run successfully after modifying some parameters in it.

Can you give me some suggestions,really thank you!

Hello,

I'm interested in how the number of histories is determined. Therefore I tried to replicate the air kerma method described in the MCGPU section. However, I'm not able to obtain the reported simulated source exposure of 3.7e-9 µGy/history for the 30kVp W/Rh spectrum.

Briefly described I've made a 10x10x10 voxel model (voxelsize 0.2mm) with 0 (=air) allocated to each voxel. I also changed the source position to 1m. With my simulation parameters, that can be found in attachment, I obtain a simulated source exposure of 5.7e-9 µGy/history. Do you any idea what I'm doing wrong? I've made no changes in the MCGPU code.

Thank you very much,
Katrien

output_projection.txt

Hi, I try to test using the VICTRE tool.
Can I use a customized phantom? For example, a rectangular cube.
In other words, how do I make a customized .raw.gz file?

Hello, I have a question about the visualization of the MD images. I am interested in obtaining a sort of "post processed" DM image, such as the one presented in one of the VICTRE articles:

I saw, in another issue, that the lesions were made more conspicuous by increasing their radiography attenuation during imaging, I think that might mean a modification of the "density" of the material indexed by 200 in the SECTION MATERIAL FILE LIST on the .in files for imaging, is this correct? Can I get more details about increasing their radiography attenuation during imaging ?

The below image is one provided, in the repository for X-ray imaging, that has a lesion (mcgpu_image_22183101_scattered_0000.raw), I played with the brightness and window level, however the inner structures of the breast or the mass are not easily identifiable.

Any extra information I can get about the post processing of the images for display purposes would be of great help. Thank you very much!