Dear Jieren,
then you should switch to 2017.07.
I am not sure which files you used to simulate your image, but the files
provided on the challenge homepage (
http://www.tractometer.org/downloads/downloads/ismrm_challenge_2015/FilesForSimulation_v1.zip)
include a mask of size 90*180*90. Probably you used the wrong mask. Where did
you obtain the 180*200*180 mask?
Best regards,
Peter Neher
<http://www.dkfz.de/>
________________________________
Von: Xu Jieren <[email protected]>
Gesendet: Montag, 25. September 2017 15:29
An: Neher, Peter
Cc: [email protected]
Betreff: Re: [mitk-users] Generating the
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?9?25????,Neher, Peter
<[email protected]<mailto:[email protected]>> ??:
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]>
Gesendet: Montag, 25. September 2017 02:31
An: [email protected]
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
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