Dear Peter,
Thanks a lot for the reply. It helps a lot. Indeed I have been running the
simulation in the version 2014 trying to have a faster implementation.
And I'll clarify the second mask question. I noticed that the dimension of
the ground truth bundles of the ISMRM 2015 data is around 180*200*180, with
an input binary mask of the same dimension. However, the simulated ground
truth nifiti files, i.e. the output of Fiberfox simulation, is of dimension
90*180*90 (parameters set for the generation signal), and this nifiti
file has no output mask (which should be of dimension 90*180*90). Since
this generated dwi data has no mask, I could not put a prior mask in
its following processing steps, e.g. the QBall image generating step or the
peaks extraction step. So I'm wondering if Fiberfox can output a generated
tissue mask of the output dimension so that those following processure are
possible, or is there a way that I could registrate the original mask to
the generated data?
Thank you.
Best, Jieren
2017年9月25日星期一，Neher, Peter <[email protected]> 写道：
> Dear Jieren,
>
> which version of MITK Diffusion are you using? The current version 2017.07
> automatically outputs nifti files:
> http://mitk.org/wiki/DiffusionImaging#Downloads
> With the old version you should be able to load the .dwi file in the GUI
> and save it as .nii, but I highly recommend updating to 2017.07.
>
> As for your second question, I am not sure what you mean by "QBall
> generating pipeline". Are your referring to the Fiberfox simulation? The
> mask for the generated file is the same as the mask for the simulation.
>
> Best regards,
> Peter
>
> ________________________________________
> Von: jierenxu <[email protected] <javascript:;>>
> Gesendet: Montag, 25. September 2017 02:31
> An: [email protected] <javascript:;>
> Betreff: [mitk-users] Generating the
>
> Dear developers,
>
> I've been trying to regenerate the ISMRM 2015 challenge data by the files
> provided on the challenge website using Fiberfox. And I went into the
> following questions,
>
> 1. The output DWI data format is .dwi, however, the given challenge data is
> several .nii files and .bvecs and .bvals. Could I use MITK transform
> between
> those two data types? If not, how could I retrieve the challenge data in
> .nii type?
>
> 2. There is a mask provided in the generating files. Could I have a
> mask.nii
> file of the generated .dwi data as well? Cause I notice that there are
> options for a tissue mask for the QBall generating pipeline.
>
> Thank you!
>
> Best regards,
>
> Jieren Xu
> Duke University
>
>
>
> --
> Sent from: http://mitk-users.1123740.n5.nabble.com/
>
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