[Mrtrix-discussion] iFOD1, iFOD2 and SD_PROB

[Donald Tournier]

Hi again,

The defaults in the new version should work well for just about any data
set - we put quite a bit of thought into this. I wouldn't change the
parameters a great deal, unless certain applications require it. For
example with short tracks TDI you would want to use a short maximum length.
Other than that, the default values really should adjust to the data set
appropriately.

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 22:15, "Manuel Blesa Cábez" <mblesac at gmail.com> wrote:

> Hi Donald,
>
> I was trying to adapt the parameters to my dataset (mouse brain), but
> after all the standard parameters show the best results. There are any
> parameter that I can play to obtain the best results? or the standard
> values show us the best results? Thanks
>
> Regards,
>
> Manuel Blesa
>
>
> 2014-06-03 19:51 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:
>
>> 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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