[Mrtrix-discussion] iFOD1, iFOD2 and SD_PROB

Wed Jun 4 08:50:10 PDT 2014

Thanks for your help!

Regards,

Manuel Blesa

2014-06-03 23:36 GMT+02:00 Donald Tournier <jdtournier at gmail.com>:

> 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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