Dear Peter,
Thanks very much for helping. Yes, I have the same file downloaded. After
switching to the latest version, I have the file generated in a
nifti format. But this step took over 10 hours on my Ubuntu.
I also figured out the reason for the dimension mismatch. I used a
vtk reader to invert the vtk ground truth file Fiber.fib to Matlab format
and it didn't interpret the dimension (~180*200*180) by the given hider.
Best, Jieren
2017-09-25 11:54 GMT-04:00 Neher, Peter <[email protected]>:
> 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]>
>> 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
>>
>>
>>
>> --
>> Sent from: http://mitk-users.1123740.n5.nabble.com/
>>
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