Convert png/JPEG to DICOM format

[SELVA MUTHU KUMARAN SATHAPPAN]

Hello Everyone,

I have a folder of png images. Each image represents skin lesion.

I would like to convert these png images to dicom format.

Can you please let me know if there any converter available to transform this png to dicom image?

Thanks

Selva

[Hiroaki Inomata]

Hi,

Many DICOM Viewers can convert .png file into DICOM file.

I developed HorliX, my customized version of Horos/OsiriX.

HorliX/Horos/OsiriX maybe can do it using plugin.
See attached files.

Then, you should transferred these dicom files into Orthanc, conquest,
dcm4chee...etc.
Ref: https://www.youtube.com/watch?v=83cSqXo_cLs

Hiroaki Inomata
MD: psychiatry
BSc: physics
PHAZOR, LLC
https://phazor.info

2019年6月25日(火) 12:11 SELVA MUTHU KUMARAN SATHAPPAN <selvasat...@gmail.com>:

> --
> You received this message because you are subscribed to the Google Groups "Orthanc Users" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to orthanc-user...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/orthanc-users/CAFpq_VWHvb6X_UyT2KSyV9O76C3QLvSxF%2BK657Tn%3DhXixZtz-w%40mail.gmail.com.

[SELVA MUTHU KUMARAN SATHAPPAN]

Hello Hiroaki Inomata,

Thank you for the help. Can I know whether the below two things is posible?

1) png to mhd format?

2) dicom to mhd format?

Is there any converter to do the same? I did search online but found something like SimpleITK which requires us to code

Thanks

Selva

[Hiroaki Inomata]

Hi,

I am not familiar with mhd format.
Could you present mhd format and associated resources on internet?


Hiroaki Inomata
PHAZOR, LLC
https://phazor.info

2019年6月25日(火) 13:09 SELVA MUTHU KUMARAN SATHAPPAN <selvasat...@gmail.com>:

[Hiroaki Inomata]

Hi,

mhd format is ITK-specific one?
Ref: https://itk.org/Wiki/ITK/MetaIO/Documentation

In that page, I fount sample .mhd like:
----------------------------------
ObjectType = Image
NDims = 3
DimSize = 256 256 64
ElementType = MET_USHORT
ElementDataFile = image.raw (this tag must be last in a MetaImageHeader)
----------------------------------

It is plain text, isn't it?

2019年6月25日(火) 13:24 Hiroaki Inomata <inomat...@gmail.com>:

[Hiroaki Inomata]

>2) dicom to mhd format?

I think that it can do in various ways.
DCMTK, well-known great free software, be able to extract DICOM tag
information from DICOM file.

You can get a number of column pixels, for example, in DICOM image
like the following code:
------------------ C++
-------------------------------------------------------------------
#include "dcmtk/dcmimgle/dcmimage.h"

........................
........................

unsigned short extractNumColumn(){

DcmFileFormat file_format;
OFCondition status = file_format.loadFile(PATHTOFILE);
std::shared_ptr<DcmDataset> dataset(file_format.getDataset());

key = DCM_Columns;
unsigned short columns =0;
dataset->findAndGetUint16(key, columns);

return columns;
}
--------------------------------------------------------------------------------------------------

Hiroaki Inomata
PHAZOR, LLC
https://phazor.info

2019年6月25日(火) 14:52 Hiroaki Inomata <inomat...@gmail.com>:

[SELVA MUTHU KUMARAN SATHAPPAN]

Hello Hiroaki,

I have attached a skin lesion image which is in png format of 2 dimensions which is  224,224. But then for color, I guess it can be 224,224,3

When I convert this to dicom, it becomes 224,224,1. How can I retain it to be 224,224,3?

img.png - 224,224,3

img_1.dcm - 224,224,1

How can I make img_1.dcm as 224,224,3?

Can you please help?

[Hiroaki Inomata]

I guess that (224, 224, 3) in mhd format is (columns, rows, a number of slices).
3 does not mean photmetricinterpretation(RGB).

2019年6月25日(火) 16:37 SELVA MUTHU KUMARAN SATHAPPAN <selvasat...@gmail.com>:
>
> Hello Hiroaki,

[Sébastien Jodogne]

Hello,

You can do this directly using the REST API of Orthanc, with URI "/tools/create-dicom". Here is a full sample script in bash:

#!/bin/bash

set -ex

IMAGE=`cat Lena.png | base64 -w 0`

cat <<EOF > /tmp/request.json

{

  "Tags" : {

    "PatientID" : "123",

    "PatientName" : "LENA",

    "StudyDescription" : "FROM^PNG"

  },

  "Content" : "data:image/png;base64,${IMAGE}"

}

EOF

curl -H 'Expect:' http://localhost:8042/tools/create-dicom -d @/tmp/request.json

Note that the integration tests of Orthanc contain more samples (notably to create a DICOM instance from a PDF file):

https://bitbucket.org/sjodogne/orthanc-tests/src/default/Tests/Tests.py

HTH,

Sébastien-

[SELVA MUTHU KUMARAN SATHAPPAN]

Hello Hiroaki,

Ahh. But can you let me know how can I generate 3 slices from one png image?

Thanks

Selva

[Hiroaki Inomata]

Do you want to get a kind of DICOM files I attached?
Ref: skin224.zip

skin3DVR.png is 3D image based on the above DICOM files.

Hiraoki Inomata
PHAZOR, LLC
https://phazor.info

2019年6月25日(火) 17:45 SELVA MUTHU KUMARAN SATHAPPAN <selvasat...@gmail.com>:

[Hiroaki Inomata]

I mistook the RGB order of the pixel in the DICOM files of previous post.
Skinrgb.zip is, maybe, correct.

skinRGB-3DVR.png is 3D image constructed by the above DICOM files.

Hiroaki Inomata
MD: psychiatry
BSc: physics
PHAZOR, LLC
https://phazor.info

2019年6月25日(火) 22:11 Hiroaki Inomata <inomat...@gmail.com>:

[Hiroaki Inomata]

Hi,

BTW, what disease does this patient have?

I suspect just a mole or melanoma but I am not sure which is correct
because I am a just psychiatrist and not familiar with dermatology.

Hiroaki Inomata
MD: psychiatry
BSc: physics
PHAZOR, LLC
https://phazor.info

2019年6月26日(水) 21:01 Hiroaki Inomata <inomat...@gmail.com>: