CODEWITHSUNDEEP
image-processingitk
Lot_to_learn
Lot_to_learn

Reputation: 622

How to change the default image viewer in SimpleITK

I am using the SImpleITK and ipython notebook for image processing and as we know imagej is the default image viewer in simpleitk. But the type of image i am using is .mha and .mha is not supported by imagej. For this I have to use fiji or imagej2.

I have tried to make fiji as a default image viewer according to the instruction mentioned in simpleitk FAQs but did not get success and show the following message: Make Fiji as default Image viewer in SimpleITK

I want to know what mistake I am doing .

How to make Fiji or imagej2 as a default image viewer for all types of images when I work with simpleitk and ipython notebook.

Thanks.

Upvotes: 1

Views: 695

Answers (3)

Dave Chen
Dave Chen

Reputation: 2085

Try changing the "%F" to "%f". It is case sensitive. Or actually, you can just leave it off. If there is no "%f" it will just put the file name at the end of the command line.

Also, you can use SimpleITK/ImageJ to view MHA files. SimpleITK actually writes out a Nifti file by default when Show is called, regardless of the input image.

Upvotes: 0

SeF
SeF

Reputation: 4160

Try to change the extension of the file with the system variable SITK_SHOW_EXTENSION and try to provide the command to the visualisation software with SITK_SHOW_COMMAND. In my .bash_profile I have:

export SITK_SHOW_COMMAND='itksnap'

Other instructions can be obtained with ?sitk.Show() .

Upvotes: 0

Piglet
Piglet

Reputation: 28940

Looks to me like you still have ImageJ in your STIK_SHOW_COMMAND variable which is not found in your fiji folder. Read the instructions again. I assume you did not follow them well enough. Your variable should contain the new image viewer and no ImageJ in a different folder.

Upvotes: 0

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