Dear Qiuting,
thank you for reporting your issue. However I wasn't able to reproduce your
issue.
I have taken the Fibers.fib and re-done your steps, however the resuls were as
expected - i.e. the number of volumes as specified in the 'Gradient Directions'
box was generated. You can switch to the Preprocessing View and select the
generated image and the table will show you the number of images (and
b-values). To inspect the different volumes you can use the slider placed below
the DataManager.
The generated signal values depend strongly on the selected parameters, with
the default parameters provided in the view, the values I've got were 1800 in
the outside and 1950-2200 in the fiber compartments. To have a 'real' outside,
you need to use some mask to restrict the signal generation, otherwise the
voxels without fibers are taken to have the isotropic signal, voxels outside a
mask will have 0.
Best,
Jan
From: Wen, Qiuting [mailto:w...@iupui.edu]
Sent: Sonntag, 19. Juni 2016 17:11
To: mitk-users@lists.sourceforge.net
Subject: [mitk-users] MITK Diffusion Fiberfox
Dear all,
I'm new to MITK Diffusion and would like to get some help in using Fiberfox.
I'd like to simulate DWIs from a fiber phantom to test our reconstruction
algorithm, and need a 1mm*3 isotropic resolution for a specific reason. I
figure the easiest way might be to use an existing fiber phantom and use
Fiberfox to simulate DWIs.
The only fiber phantom data I could find online is the "ISMRM 2015 Tractography
challenge - Data" from http://www.tractometer.org/ismrm_2015_challenge/data
which published all files needed to regenerate DWIs e.g. Fibers.fib. However,
the output DWIs only has one volume.
The steps I did was:
Open MITK Diffusion 2014.10.02, switch to fiberfox module, load Fibers.fib. In
the Signal Generation tab, I entered Image settings to the desired #directions
and b-values, along with others. Then I select the Fiber.fib image and start
simulation. When simulation is done, I save the .dwi outoput file to .nii,
which only contains one volume (asking for 10 directions) and the contrast
looks a bit weird: with intensity ranges from 204-242 and none fiber regions
being all 204.
Could you anyone help give me some suggestions on what I did wrong?
Thanks,
Qiuting
------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
mitk-users mailing list
mitk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mitk-users
