All Questions
Tagged with dicom image-processing
83 questions
0
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1
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42
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Duplicate Frames When Converting NIfTI to DICOM SEG Using itkimage2segimage [closed]
I'm converting a NIfTI file with multiple segmentations (e.g., Liver and Spleen) into a DICOM SEG file using the itkimage2segimage tool from dcmqi.
For example:
Input NIfTI: 203 slices with 2 labels (...
0
votes
1
answer
257
views
Window width and Center and Hounsfield units [closed]
I am currently adjusting the brightness and contrast of a grayscale image using fo-dicom.
Loading the image:
_dicomFile = DicomFile.Open(GetImageFileName());
_dicomImage = new DicomImage(...
0
votes
1
answer
472
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Invert grayscale using fo-dicom
I'm currently using fo-dicon to build a simple dicom viewer in C#. I am currently increasing or decreasing the brightness and contrast by adjusting window width & center values.
How do I invert ...
3
votes
1
answer
905
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How to get color depth of DICOM pixel data in reliable way?
A DICOM file may have either uncompressed pixel data or compressed pixel data. It's PhotometricInterpretation (0028,0004) can be MONOCHROME1/MONOCHROME2/RGB/PALETTE COLOR/YBR etc. There is also a ...
- 265
0
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1
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2k
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How to save DICOM in same series using pydicom [duplicate]
I have saved the Preprocessed DICOM in a folder total of 300 .dcm files, but when I open this DICOM folder path in RadiANT DICOM Viewer only One slice is displayed, here is my code is attached, Can ...
- 17
0
votes
1
answer
826
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DCMTK library says tag not found while dcmdump displays it
My program, for a Ubuntu 20 system using DCMTK 3.6.4-2, reads a dicom file (series) and gets the scale slopes from the corresponding tags, testing first whether they exist:
tmpfile.loadFile ( filename ...
- 2,480
0
votes
1
answer
228
views
Imebra library shows completely gray image for transfer syntax 1.2.840.10008.1.2.1
Iam trying to use Imebra library to display DICOM images in android. Iam using version 5.0 of the library.
The bitmap shown is completely gray, transfer syntax for image is 1.2.840.10008.1.2.1.For ...
- 54
2
votes
1
answer
1k
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How to transform stored values in a DICOM file to real world units?
I am trying to calculate radioactivity concentrations on a PET DICOM image using either Matlab or python. I have read in the DICOM standard that
(0028,1053) Rescale Slope
(0028,1052) Rescale ...
- 107
1
vote
1
answer
435
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how to write multiple dicom files into a folder using 'dicomwrite' command
using for loop, i can read all the 'k' dicom files present in the folder . After performing some operation on each slice, i need to save them into another folder .
Someone please help me
names=dir(...
- 67
3
votes
2
answers
3k
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Medical Image quality problem with DICOM files
I am trying to make some segmentation tasks on CT images which are in DICOM format, using python.
The main problem is that when I am trying to read the DICOM file (https://www.dicomlibrary.com/...
- 83
4
votes
2
answers
1k
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Can Hounsfield Units be shifted?
I'm working on some chest scans from the LIDC database, I am trying to apply iterative (optimal) thresholding on them to extract the lung area.
Many researchers use an initial threshold of (or around -...
- 390
1
vote
2
answers
622
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How to calculate Temporal Resolution without DICOM header?
How can I calculate the Temporal Resolution of MRI sequence if it's not written in DICOM header?
What other DICOM information can I use to calculate out the temporal resolution?
It might worth ...
- 121
1
vote
2
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5k
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Saving DICOM image as lossless JPEG
My original image is in DICOM format and I want to save it in lossless jpg format (or at least keep as much information as I can!!!). How can I do that in python? Currently, I am using the following ...
- 1,286
0
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2
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2k
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Processing Xray Images (.dcm files) using pydicom (could not find SliceThickness Attribute)
I am new to Image Processing and want to know how can I pre-process dicom images using python. I am following the below tutorial:dicom in python I do not have the SliceThickness attribute in my data. ...
- 593
5
votes
2
answers
384
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Performance issue with reading DICOM data into cell array
I need to read 4000 or more DICOM files. I have written the following code to read the files and store the data into a cell array so I can process them later. A single DICOM file contains 128 * 931 ...
- 275
3
votes
1
answer
1k
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How to read a dicom file on matlab?
I have a dicom file of size 256*256*3. However, when I read this file using dicomread command in matlab the size of the dicom file is 256*256? How to fix this ?
`close all;
clear all;
clear all;
%...
- 75
0
votes
1
answer
399
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Reading .dcm files itk
I am using itk library for reading my .dcm files using its example in: https://itk.org/Doxygen46/html/IO_2DicomImageReadWrite_8cxx-example.html.
When I use CMake to build this example its appear that ...
- 51
2
votes
2
answers
3k
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How are the spacing value of the z dimension and thickness (0018, 0050) different in dicom series?
I've been studying some dicom series and find that the thickness attribute and the itkimage.GetSpacing()[2] value are not always consistent.
For example the thickness (0018, 0050) value encoded in ...
- 1,900
1
vote
1
answer
561
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EvilDicom Image Corrupted
I'm trying to use the library to anonymize a dicom image.
In some cases it works fine, but in other cases the final image is corrupted. I mean, the pixels of the image are wrong and also the ...
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-1
votes
1
answer
345
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How to extract features from a 3D Dicom Image
I am working on a project that needs to extract features from the medical images (.DICOM). I am working on Borland C++. I have never worked on such a project. Can you provide me some useful resources ...
- 37
0
votes
1
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178
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How to apply a function to a series of CT dicom images in Matlab?
Am new to matlab and am trying to write a code that converts CT lung DICOM images to Hounsfield Units(HU). I've already created a function to do so and saved it in an M-file. I would like to know how ...
- 1
4
votes
2
answers
2k
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Difference between dcm2pnm, dcmj2pnm and dcml2pnm
The title says it all. What is the difference between dcm2pnm (http://support.dcmtk.org/docs/dcm2pnm.html), dcmj2pnm (http://support.dcmtk.org/docs/dcmj2pnm.html) and dcml2pnm (http://support.dcmtk....
- 24.5k
0
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1
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730
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Matlab: Saving multiple Dicom files as jpeg or png format
I can read a Dicom format file and display it using imshow(). Then, manualy I can save the file into jpeg or png using saveas option. This works for one file at a time. However, I have around 1000 ...
- 989
1
vote
1
answer
149
views
From image to vector and vice versa, rotated image
I read a DICOM image and for a variety of reasons, I had to turn the image matrix in a row vector.
After performing various operations on the bits of the vector, I need to reprocess the vector in a ...
user7558372
3
votes
2
answers
1k
views
DICOM file with CT and MR tags
A DICOM file (an artificial axial slice) has been generated from both a CT and an MR images. Can the aggregated file contain both CT and MR DICOM tags? E.g. Echo Time (0x18, 0x81) and KVP (0x18,0x60)?
...
- 1,337
1
vote
1
answer
1k
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Calculate Windowing in DICOM
I'm implementing a DICOM-Image Viewer in C#. I don't (because I'm not allowed to) use any frameworks or libraries that do the image processing for me.
With which algorithm can I calculate the ...
0
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1
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467
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Error: The compressed pixel data is missing item delimiters.?
I am working with few Dicom files and when i try to use dicomread('filename.dcm') in MATLAB it gives the following error:
Error using dicomread>processOffsetTable (line 943)
The compressed pixel ...
- 369
5
votes
6
answers
4k
views
remove pixel annotations in dicom image
I am analyzing medical images. All images have a marker with the position. It looks like this
It is the "TRH RMLO" annotation in this image, but it can be different in other images. Also the size ...
- 3,640
5
votes
2
answers
3k
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convert 16 bit grayscale DICOM image to 8 bit: the correct procedure
I have been trying to create an image viewer for DICOM image. My program reads all the 8 bit colour and grayscale image almost correctly. But when I try to open a 16 bit image using the first 8 bits ...
- 81
1
vote
1
answer
2k
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How to save DICOM image as JPEG without losing information
I have a dicom image that when I open it in MATLAB it is like this:
However when I see that via dicomviewer it is like this:
How can I save these dicom images without loosing their information in ....
- 229
0
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3
answers
2k
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How to change pixel intensity range of the image in matlab?
I read dicom Image in matlab.
Pixel intensity range is really large.
I want to rescale Pixel intensity to 0 - 1000.
How Can I modify the Image ?
I would appreciate for any help please.
- 141
1
vote
1
answer
1k
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vtkResliceImageViewer display incorrect (too dark) dicom image
I am using vtkResliceImageViewer vtk library class to display DICOM files. Images are too dark. I don't know if I use it wrong way or it's a bug (there was similar unresolved problem posted before: ...
- 221
2
votes
1
answer
619
views
Octave 4.0.1 octave forge dicom package fatal error on install openSUSE linux
I am using:
linux openSUSE Tumbleweed
octave-4.0.1
gdcm-2.6.3
I have recently gotten into using linux for my research in university. For this research, I have been trying to install the dicom ...
- 23
4
votes
2
answers
984
views
Ellipsoid fitting for 3D data on matlab
I am working on a 3D volume of CT lung images, In order to detect nodules I need to fit an ellipsoid model for each suspected nodule, How can I make a code for that ???
Nodule is the suspected object ...
-1
votes
1
answer
1k
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Eliminate connected component in 3d volume matlab
I have a CT lung 3d volume, I am using matlab to extract nodules and classify it ...
I need to eliminate "delete" the air ways from the volume, in order to minimize suspected nodules, there is a ...
1
vote
1
answer
181
views
Incorrect pixel value from data cursor on Matlab
When I open a Dicom image on Matlab (R2014b) and place the data cursor on a specific set of coordinates, I obtain an "index" (or pixel value) that does not match the same set of coordinates on the ...
- 9,909
1
vote
2
answers
3k
views
how to write a read DICOM file using VTK or ITK libraries?
I used vtkDICOMImageReader to read the DICOM file. I used the vtkImageThreshold to threshold a CT image. And now i want to write it back to my hard disk before further processing.
I tried ...
0
votes
1
answer
119
views
How to understand the DICOM tag 0040,db73 ? How to validate if the values are correct?
I am working on one of the issue with the SR. The issue is happening with the values of the dicom tag 0040,db73 (referenced content identifier). Tried to understand from the standard document but did ...
- 395
0
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1
answer
712
views
how to resolve index exceeds matrix dimensions in matlab?
I am trying to read series of dicom images from a folder named as series 8.below is code to read series of dicom images from a particular folder.i am getting error index exceeds matrix dimensions at ...
-2
votes
1
answer
1k
views
How can I convert Dicom directory (series of dicom images) to 3D volume image?
I have almost 80 dicom images in a folder. Now, I want to convert these series of dicom images to a 3d volume.
Below is the code which loads MRI data, forms counter slices and then generates 3d ...
7
votes
3
answers
2k
views
DICOM Deflated Explicit VR Little Endian (1.2.840.10008.1.2.1.99)
How is the data in this transfer syntax organized? A description from the standard:
This Transfer Syntax applies to the encoding of the entire DICOM Data Set. The entire Data Set is first encoded ...
- 12.3k
0
votes
2
answers
220
views
Mid line through a set of dicom images in matlab
I have a set of Dicom images on matlab and i would like to add a midline going through all the images
I am outputting the images via imshow3d function
thanks
Edit: here's what i have, the random ...
- 615
2
votes
1
answer
969
views
What does the index refer to when selecting a pixel on an image in Matlab?
When looking at a single pixel of an image in Matlab, what does this index refer to? X/Y refer to the coordinates of the pixel, and RGB refers to the color, but any ideas on what the index is?
To ...
2
votes
1
answer
804
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Problems Applying MATLAB Filters to Dicom Images
I am working with dicom chest PA's. I have no problem loading the images and doing basic thresholding work, however I need to apply some filters. I will be designing my own filters in the future but ...
- 536
0
votes
2
answers
3k
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Assign the Window centre and window width for dicom image
I have a Dicom image file in dcm format.In matlab by using Dicomread i got image data and by using dicominfo i got window center and window width of that dcm file. Now i want to display the image by ...
- 396
0
votes
2
answers
3k
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Easy way to calculate the shift between two arrays? Python
I have two dicom images and can compute the mean squared error of the images using the code below. However, there can be an inherent shift in one image compared to another (if my imager is slightly ...
- 478
0
votes
1
answer
514
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How to connect a set of DICOM images to its Scout image?
Given a set of images I have to find the scout image which contains that set. Now I'm using study ID (0020,000D) and Scan Option (0018, 0022): when set_of_images.StudyID=x.StudyID and x.scanOption="...
- 49
0
votes
2
answers
771
views
how to modify image pixels in DICOM files using Imebra library?
I use Imerba library to read DICOM files.
I need acces to pixels so I can modify them in low level.
Documentation says: "In order to access to the image's pixels you have to retrieve a data handler"
...
- 54
4
votes
1
answer
5k
views
How to save image as DICOM
I need to save JPEG image as a DICOM using c# and some free library. I read a lot of topics where it was described how to do the opposite, but I couldn't find anywhere how to perform what I need. The ...
- 572
1
vote
1
answer
2k
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How to change gray level of Dicom image?
I am working gray images in which gray level lies 0 to 255 . I want to work on Dicom images but maximum gray level of dicom image is grater than 255. I just want to know that how to change dicom image ...
- 13