[Mrtrix-discussion] iFOD1, iFOD2 and SD_PROB

[Donald Tournier]

Hi Manuel,

Any particular reason for the non default parameters for the tracking?
These values would be appropriate for iFOD1, but iFOD2 expects larger step
sizes and much larger angles. In fact, your angle parameter is itself far
too small - value are in degrees, not radians. A sensible value for iFOD1
would be 10 or 20, larger again for iFOD2. Try using the defaults for
everything, see if that still produces odd results.

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 18:29, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:

> 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
>>>
>>>
>>> _______________________________________________
>>> Mrtrix-discussion mailing list
>>> Mrtrix-discussion at www.nitrc.org
>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>
>>>
>
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