Problems saving transformed file

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Problems saving transformed file

Jasper Helthuis

Dear all

 

I'm new to 3DSlicer and to using a mailing list (so exiting day!).

 

I have two source images with different resolutions from the same sample. I first used a transform on the moving image to manually rotate both images to roughly align (needed rotation of at least 90 degrees around two axes). I hardened the transform. I then used the General registration (BRAINS) module to automatically register the two images. I hardened the transform on the moving image.

Next I used the Crop Volume module to select an ROI to crop the exact same region in both scans. I saved both files using file>save to .img Analyse75 files.

If I open those resultant img files in 3DSlicer and overlay those they match perfectly.

 

However if I open both in imageJ or MevisLab both images do not overlay correctly and the first manual transform is also lost (so both images are not rotated 90 degrees around two axes).

 

What am I doing wrong on saving from 3DSlicer, because slicer shows both images matching but ImageJ does not?

I tried saving in different file formats which does not seem to help.

 

Any advice would be greatly appreciated.

 

 

Kind regards,

Jasper



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Re: Problems saving transformed file

inorton

On Fri, Sep 30, 2016 at 7:30 AM, Jasper Helthuis <[hidden email]> wrote:

Dear all

 

I'm new to 3DSlicer and to using a mailing list (so exiting day!).

 

I have two source images with different resolutions from the same sample. I first used a transform on the moving image to manually rotate both images to roughly align (needed rotation of at least 90 degrees around two axes). I hardened the transform. I then used the General registration (BRAINS) module to automatically register the two images. I hardened the transform on the moving image.

Next I used the Crop Volume module to select an ROI to crop the exact same region in both scans. I saved both files using file>save to .img Analyse75 files.

If I open those resultant img files in 3DSlicer and overlay those they match perfectly.

 

However if I open both in imageJ or MevisLab both images do not overlay correctly and the first manual transform is also lost (so both images are not rotated 90 degrees around two axes).

 

What am I doing wrong on saving from 3DSlicer, because slicer shows both images matching but ImageJ does not?

I tried saving in different file formats which does not seem to help.

 

Any advice would be greatly appreciated.

 

 

Kind regards,

Jasper



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slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ