MIAS mammographic image analysis society

Thank you Mr. Eltoukhy,

Sir,

I saw your papers, you are doing an excellent effort. As far as I know from the literature, MIAS has less cases as compared to DDSM database. I was successful downloading a few images from DDSM database using the CygWin software that emulates the Unix environment in Windows. Now I am a bit stuck up with opening the groundtruth files in Matlab. There is a code for matlab with the name get_ddsm_groundtruth.m with which one can download the DDSM Radiologist Annotations and Metadata. However it is giving errors. If anyone has worked on that please do share.

Regards.

Arbab Masood Ahmad

Hi Mr. Masood

Sir,

Could you please tell me how to use CygWin software to download images from DDSM database o n windows 7, i have install it but it give error.

Hi, Shaymaa.

The manual that you must have downloaded with the software has very good instructions. You must follow those instructions carefully and let me know where you get stuck up. You must also be careful with the file names that are mentioned in it. To avoid typing errors a better option is to copy and paste the name in the command line. Often the server is busy and you get errors. For this try the download at some other time. I managed to download one or two images and the associated groundtruth files sometime ago.

Thank you Mr. Masood

I follow the instructions but in the step (9. Under the Devel category, choose to install Ruby) i have not found Ruby here, i found it as a separate Package and i choose to install it, but the error begin in step (18. Verify that the Ruby program was installed correctly; type the following and press return:

ruby -e “p ‘Hello world!’”) , the error is

[$ ruby -e “p ‘Hello world!’”

-bash: !’”: event not found

i do not know what is the problem, could you help me

I have some Mammogram image data in .pgm format. whether .pgm format is useful for you or not?

.pgm is format for gray scale image.

Try this site

http://microserf.org.uk/academic/Software.html

This is the same site i have used

For the point you were stuck up in, do the following:

(1) Under Graphics category select package: Image Magick: Image manipulation software suite.

(2) Under Devel category select package: subversion Ruby: A version control system(ruby binding).

The rest should work fine, try it and let me know.

For the point you were stuck up, select the package: subversion Ruby: A version control system(ruby binding).

The same error still exists

One of the sources of data is the following. You can request the university and they will send you the licence key to download the data for non commercial use,

http://ganymed.imib.rwth-aachen.de/irma/datasets_en.php?SELECTED=00010

Yes, this data set is free and you can get it once you send the agreement letter to the given address.

I got the dataset from 

http://ganymed.imib.rwth-aachen.de/irma/datasets_en.php?SELECTED=00010

but it does not include the overlay images. I tried to access DDSM but never succeeded. Has anyone tried DDSM recently? Or does anyone have the overlay images for DDSM?

Dear Noorul Wahab,

You can directly download the the overlay file for the view you like by opening the ftp with each case on the DDSM site:

http://figment.csee.usf.edu/Mammography/Database.html

The overlay files exist only for cancer and benign cases. For example following is a link to case 0001:  

ftp://figment.csee.usf.edu/pub/DDSM/cases/cancers/cancer_01/case0001/ 

after opening the page right click the file with .overlay extension and save as type .overlay. Once you have done that, there are Matlab commands whereby you can extract the region of interest represented by the overlay file. You can see my recently  published paper on the following link: 

http://link.springer.com/chapter/10.1007%2F978-3-662-44654-6_20

Please feel free to ask if any thing is not clear in the paper.

Thanks and Regards.

Arbab Masood Ahmad 

Dear Masood,

Thanks, that worked. I have attached a screenshot of what I got with get_ddsm_groundtruth.m for case C_0001_1.RIGHT_CC.OVERLAY? It doesn't overlay on  the image as are show in the thumbnails of DDSM website where the suspected regions are circumscribed. I am relatively new to image processing.

I do not have access to your paper.

Do you use your UET email?

Regards,

Noorul Wahab

Hi Mr. Shaymaa Ahmed 

I can solve your problem with the error in step (18.  You just need to type a space keyboard between the ! and ' , then it will work. But I don't know the reason. 

ruby -e “p ‘Hello world!’”  →  ruby -e “p ‘Hello world! ’”

And I also successfully used the below website to convert  .LJPEG to .PNG .

http://microserf.org.uk/academic/Software.html

( My OS is Windows 8, but when I typed the instruction "get-ddsm-mammo", it didn't work to convert the Image. 

So I tried to use VMware to install Windows_XP_Professional_SP3, and it worked !! )

Now, I start to tell you how to convert Image.

Step (1.  Download the .LJPEG that you want (I will use C_0051_1.RIGHT_MLO.LJPEG as Example!) from the DDSM. Then copy the .LJPEG file to the "ddsm-software" directory.

Step (2. Open your Cygwin and change to the "ddsm-software" directory.

Step (3. Type instruction "./jpeg.exe -d -s C_0051_1.RIGHT_MLO.LJPEG", then you should see the file "C_0051_1.RIGHT_MLO.LJPEG.1" be created in the ddsm-software directory.

Step (4. Type instruction

"./ddsmraw2pnm.exe C_0051_1.RIGHT_MLO.LJPEG.1 4680 2736 lumisys".

4680 is rows, 2736 is columns and lumisys is digitizer. Digitizer is one of "dba", "howtek-mgh" , "howtek-ismd" and "lumisys". Once you have done that, you should see the file "C_0051_1.RIGHT_MLO.LJPEG.1-ddsmraw2pnm.pnm" be created in the directory.

Step (5. Type instruction

"convert.exe -depth 16 C_0051_1.RIGHT_MLO.LJPEG.1-ddsmraw2pnm.pnm C0051.png". And it's totally complete, you will get PNG Image in the directory.

In Step (4 , the information of rows, cols and digitizer can be known in .ics file.

Thanks and Regards.

Chi-Fan Wang

Hello, 

I have written a small utility to easily download, convert, view and get annotations from DDSM data, without the need for any manual work. You just need to download the required cases and then follow the instructions on how to use my utility to convert the LJPEG files to LJPEG1 and then to other formats like PNG, JPEG, TIF, GIF etc. 

You can download my utility from here - https://github.com/trane293/DDSMUtility 

The detailed instructions along with images are given in the Tutorial PDF file. 

Please revert back to me if you have any questions or problems. 

Hi Dr. Anmol Sharm

Your software is so good i have download some cases from ddsm database and convert it to png format using it, thanks. Could you please tell me how to convert it to jpg?

Hi Chi-Fan Wang !

Do you have the images of DDSM data base.

I am doing research work in breast cancer diagnosis based on fusion of texture features from MLO and CC view mammograms. Now the

websites

http://marathon.csee.usf.edu

http://ganymed.imib.rwth-aachen.de/irma/datasets_en.php?SELECTED=00010

are not opening.

Hence, if you have this data, help me by sharing that data, it will very much useful for my research.

The data is many hundred GB so I am afraid it is not possible to send through e-mail or other means. Moreover it was acquired under an agreement with the university of Aachen so sharing would be illegal.

The data can be downloaded from The Cancer Imaging Archive database.

https://pdfs.semanticscholar.org/fa8b/2ab09d8b940f2ed02aca10dc0d23fd893a63.pdf

https://pdfs.semanticscholar.org/4bb9/3516e0da3c234c97e358849d324d5c6797d9.pdf

https://ac.els-cdn.com/S1877050915018700/1-s2.0-S1877050915018700-main.pdf?_tid=157ff912-59b9-4ae5-b828-79d5e05dd4cf&acdnat=1525093312_7a31e4bfdc2b2d24f02e69cc098cd16e

A curated version of the DDSM is freely available on The Cancer Imaging Archive: http://dx.doi.org/10.7937/K9/TCIA.2016.7O02S9CY

How could we get the CBIS-DDSM ground truth?