about exporting segmentation from ITK-SNAP

[Daniel Yan]

Hi,

I am currently using MaZda (http://www.eletel.p.lodz.pl/programy/mazda/) to do texture analysis. But the segmentation function in MaZda is difficult to use. I am wondering if I can segmentat the images in ITK-SNAP, and then export the segmentation to files that can be load in the MaZda software? The filetype of segementation used in MaZda is .roi.

I would be appreciated if anyone can help.

Thanks in advance!

Daniel

[Paul Yushkevich]

Hi Daniel,

I have no experience with Mazda and their ROI format. I would contact them to see if they offer some conversion tools. If you save an image as an MHD image in ITK-SNAP, it creates a header file and a raw data file that might be possible to convert into a Mazda ROI with some tweaking. 

Paul

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[Daniel Yan]

Hi Paul,

Thank you for you help. Piotr have emailed me and offered helpful advice.

I exported the segmentation from ITK-SNAP as nii.gz file,  then converted nii.gz to PNG files (using convert3D); and then I wrote a script to conver PNG to BMP, which can be loaded into MaZda as ROI.

Thank you again for your help!

Warm regards,

Daniel

On Thursday, January 26, 2017 at 1:22:46 AM UTC+8, Paul Yushkevich wrote:

Hi Daniel,

I have no experience with Mazda and their ROI format. I would contact them to see if they offer some conversion tools. If you save an image as an MHD image in ITK-SNAP, it creates a header file and a raw data file that might be possible to convert into a Mazda ROI with some tweaking. 

Paul

On Wed, Jan 25, 2017 at 12:27 AM, Daniel Yan <yan...@gmail.com> wrote:

Hi,

I am currently using MaZda (http://www.eletel.p.lodz.pl/programy/mazda/) to do texture analysis. But the segmentation function in MaZda is difficult to use. I am wondering if I can segmentat the images in ITK-SNAP, and then export the segmentation to files that can be load in the MaZda software? The filetype of segementation used in MaZda is .roi.

I would be appreciated if anyone can help.

Thanks in advance!

Daniel

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[Urs Jacob Mühlematter]

Dear Daniel

Many thanks for sharing your information. I have a similar problem, however, I need to transform the ROIs from MaZda to a format that can be read in matlab. I tried to rename the .roi to .bmp and transform them to png using python. However, it did not work. Do you have any idea how I could do that?

Many thanks for your answer,
Urs

[mfk16]

The updated program can now take input user defined ROIs as .nii files!