I2CVB Prostate (12 subjects)

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#1

Dataset Description:
A dataset containing multi-parametric MRI datasets with zone labels for the development of computer aided detection and diagnosis technology.

Imaging Data:

  • Multi-parametric MRI.
  • Ground truth prostate zone contours.
  • 1.5T and 3T scanner data.

Number of subjects / images: 12 subjects.

Link to dataset / homepage : http://i2cvb.github.io/

1 Like
#2

Hello, I have tried to download the data to train in a U-net algorithm but each single data comes in different file format that I am not familiar with and not DICOM as stated in the description.
please help me with the method I can use to transform the data to DICOM format

#3

Hi there,

Welcome to imaging QA — thanks for contributing!

I believe that you are downloading the files with names ending .aa, .ab, .ac, etc. If this is the case, these are all parts of the same .zip file that has been split for upload. Once you have downloaded a set of fileparts they will need to be recombined first using the cat Linux/Unix command line tool, then unzipped. See example below.

For the GE data named ge-1-5t.aa, ge-1-5t.ab etc :

  1. Recombine using command ‘cat ge-1-5t* > ge-1-5t.zip’
  2. Unzip ge-1-5t.zip

I hope this works for you.

#4

thanks, i managed to recombine the zip file i get this error when i attempt to unzip it
Archive: ge-1-5t.zip
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip: cannot find zipfile directory in one of ge-1-5t.zip or
ge-1-5t.zip.zip, and cannot find ge-1-5t.zip.ZIP, period.

i have tried online solutions to try and fix it but i have been unsuccesful

#5

These are actually not .zip files, they are .tar.gz files. The correct commands are:

  1. ‘cat ge-1-5t* > ge-1-5t.tar.gz’
  2. ‘tar xzvf ./ge-1-5t.tar.gz’

I’ve just tried this with the ge-1-5t.aa …ge-1-5t.ag files downloaded from here : https://zenodo.org/record/162231#.YIciqBNKgci and it worked.

Let me know if this works for you…

#6

thanks alot, it worked… I will inform you on the progress of the projects too

1 Like
#7

Hi Kulwa,

I was wondering how you got on with this dataset. Is the image quality high? Would you recommend it to others?

Thanks,

James

#8

Hi, I am trying to do the same with GE datasets, but it did not work, do you have the datasets ready to download without this step, specially for windows users.

#9

Hi, I am trying to download GE datasets, but they seem that they are in auditable format, do you have them in DICOM format?

#10

Hi @MRMR, have you tried using the copy command to combine on windows? Then you should be able to untar using winzip or 7-zip ( think this tool can be used to combine fileparts too).

Try the copy command (or similar) in DOS to combine files ( only fileparts aa and ab in example - you’ll need to add up to ag )

copy /b ge-1-5taa + ge-1-5tab ge-1-5t.tar.gz

#11

Yes, I tried but I am not sure why it does not combine them, can you check the attached picture?

image
image1920×1080 186 KB

Thank you!

#12

Also, does the ground-truth segmentation available for these data?

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