Thanks Caspar,

That was what I wanted (to know that .fslgz is the same as .nii.gz)!!

Cheers,
Ellankavi

Von: Goch, Caspar Jonas [mailto:c.g...@dkfz-heidelberg.de]
Gesendet: 13 September 2016 13:13
An: Ramasamy, Ellankavi; 'mitk-users@lists.sourceforge.net'
Betreff: AW: [Fiberfox] Save fiber bundle as *.nii.gz

Hi Ellankavi,

unless I am mistaken the generation should result in one entry in the 
datamanager?

Just to be sure we are talking of the same thing, here the workflow I am 
looking at:

1.       Start MITK Diffusion

2.       Click on "Start Simulation" in the Signal Generation tab

3.       Draw two circles in the top/bottom slice of the dummy image in the 
Fiber Definition tab

4.       Select the dummy image and the fiber bundle and click "Start 
Simulation" in the Signal Generation tab

5.       You now should have a diffusion image (in my case 
Bundle_0_D12-12-3_S2-2-2_b1000_StickBall_RELAX)

6.       You can slide through the diffusion image directions using the Channel 
slider below the datamanager

You can now save the diffusion image by right click->Save on it. If you select 
"Diffusion weighted image" as type and change the extension to .fslgz it will 
be saved nifti conform (basically .fslgz is a renamed .nii.gz and has the 
necessary meta files (bvecs and bvals)). The custom file extension was 
necessary for our old reader/writer system to signal it being a diffusion 
weighted image. That file will contain all directions and b-values.

Best,
Caspar

Von: Ramasamy, Ellankavi [mailto:ellankavi.ramas...@ipa.fraunhofer.de]
Gesendet: Dienstag, 13. September 2016 12:25
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] [Fiberfox] Save fiber bundle as *.nii.gz


Hello,

I'm working with Fiberfox v2014.10 and I've a question regarding saving fiber 
bundles.

I'm creating a phantom diffusion image with 12 gradient directions. After 
creating the fiber bundle,
instead of scrolling through each of the 13 (12 gradients + 1 b0 image), 
right-clicking on the fiber
bundle and saving them as *.nii file, is there a way I can save *ALL* the 13 
diffusion images in one go?

Thanks

Warm regards,
Ellankavi

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