[Mrtrix-discussion] iFOD1, iFOD2 and SD_PROB

[Manuel Blesa Cábez]

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
>>>>
>>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20140603/0276d864/attachment.html>