[Mrtrix-discussion] iFOD1, iFOD2 and SD_PROB

[Manuel Blesa Cábez]

Hi Donald,

I used for all the steps of the reconstruction of thr ODFs MRtrix3.

The command line that I used is

dwi2response dwi.mif response.txt -mask mask.mif -grad
ag140113a_6_HARDI_KO_ref.b -lmax 8

dwi2fod dwi.mif response.txt fod.mif -mask mask.mif -grad
ag140113a_6_HARDI_KO_ref.b -lmax 8

tckgen fod.mif tracks2_CC1_27.tck -algorithm iFOD2 -grad
ag140113a_6_HARDI_KO_ref.b -seed_image roi2_CC1_27.mif -mask mask.mif
-number 10000 -step 0.14 -minlength 7 -angle 0.70

The voxelsize is 1.4x1.4x2.8

With the ODF viewer I can't see any strange. I changed the algorithm to
SD_stream and I think that the result is good. Thanks in advance.

Regards,

Manuel Blesa


2014-06-03 18:46 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:

> Hi Manuel,
>
> Yes, iFOD1 is almost identical to streamtrack's SD_PROB. I'm surprised
> you're getting unrealistic results with either iFOD1 or iFOD2 though, they
> have both been working well for years now with default parameters. Are you
> sure you don't have similar issues using the same data set with
> streamtrack? There is the slight issue that the FODs would need to be
> either converted using sh_basis or computed separately for each command due
> to the change in SH basis, but I wouldn't expect even that to cause grossly
> unrealistic results. Do the FODs obtained using dwi2fod look convincing
> when displayed in MRView's ODF display tool? Maybe it would help of you
> posted the commands you used to generate the FOD images and for the
> tracking, and also provide some information as to the data acquisition
> parameters?
>
> Cheers,
> Donald
>
> --
> Dr J-Donald Tournier (PhD)
>
> Senior Lecturer, Biomedical Engineering
> Division of Imaging Sciences & Biomedical Engineering
> King's College London
>
> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
> Thomas' Hospital, London. SE1 7EH
> T: +44 (0)20 7188 7118 ext 53613
> W:
> http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
>
> On 3 Jun 2014 17:20, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:
>
>> Dear all,
>>
>> I have a little question about the different propagation algorithms:
>>
>> I Know the difference between iFOD and iFOD2, but I would like to know
>> which is the difference between this last algorithms of MRtrix 3 and the
>> SD_PROB of MRtrix 2. I believe that the iFOD1 is the same of SD_PROB, I'm
>> right about this?
>>
>> In order to perform a realistic tractography, which should I use? because
>> I tried iFOD1 and iFOD2 and I obtained very unrealistic results, maybe is
>> for the parameters that I choosed, but I'm not sure. Thanks in advance.
>>
>> Best regards,
>>
>> Manuel Blesa
>>
>>
>> _______________________________________________
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>> Mrtrix-discussion at www.nitrc.org
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>>
>>
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