[Mrtrix-discussion] Facial Nerve Tractography

Tue Mar 24 08:43:34 PDT 2015

Hi Matthieu,

I think that looks like a fairly impressive delineation already. The issue
in this region will be one of susceptibility-induced distortions and signal
dropout - not much that can be done without improving the imaging itself. I
notice you're using a fairly basic acquisition (32 DW directions, b=1000,
2x2x2 resolution). If you really want to track such a small structure in
such a difficult area to image, I think you'll need to increase all of
these parameters... At the very least, try increasing the b-value to 2000,
the number of directions to 64 (if not more - it's always good to have
additional SNR), and potentially try to increase the resolution - although
that last one will be difficult to achieve, since increasing the resolution
will very quickly worsen your SNR and image distortions. You may be able to
overcome some of these difficulties using parallel imaging, but assuming
you only have access to product sequences, you may not be able to get much
better resolution than what you have already... If you need to compromise,
I think I'd go for more directions and a higher b-value over higher spatial
resolution.

The other thing to try is reducing the FOD threshold when tracking (the
-cutoff option in streamtrack). This might allow the tracking to bridge the
gap, but will come at the expense of a lot more noisy tracks in the output.
So this would only really work in conjunction with fairly restrictive
include/exclude ROIs...

Otherwise, Ivan is right that much of the discussion has now shifted over
to the MRtrix3 forum, but this is still the right place to ask questions
related to the 0.2.x version, no problems there.

Cheers,
Donald.

On 24 March 2015 at 11:02, Matthieu Vanhoutte <matthieuvanhoutte at gmail.com>
wrote:

> Dear experts,
>
> As recommended by Ivan, I will try to include more details on my post.
>
> I am using MRtrix2 et trying to tract facial nerve (VII) from the internal
> auditory meatus to brainstem. I am using CSD tracking ans SD_PROB as
> method. My seed ROI have been defined on the T1 anatomical then register on
> DTI image (32 directions images, b0 = 1000, resolution = 2x2x2).
>
> As you can see in the joined files, facial nerve on the left hemisphere is
> visible on T1 anatomical (show focus) however my tracking results show a
> hole (show focus) in the facial nerve tract.
>
> Many thanks in advance for helping !
>
> Best regards,
>
> -------------------------------------
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-24 11:06 GMT+01:00 Ivan Alvarez <ivan.alvarez.11 at ucl.ac.uk>:
>
>>  Hi Matthieu,
>>
>> This mailing list has been largely superseded by a Google+ page here:
>> https://plus.google.com/communities/111072048088633408015
>>
>> Also, if you would like some advice from the community I would recommend
>> including the following details in your post: 1) what exact structure are
>> you attempting to track? A particular branch of the facial nerve, or the
>> whole thing? 2) what method are you using? (tracking algorithm,
>> seed/waypoint ROIs, location), 3) what dMRI acquisition are you using?
>> (resolution, b values, etc.) and most importantly, 4) what makes you say
>> the results are not convincing? in other words, what's going wrong?
>>
>> Also, since you're writing here I'll guess you are using MRtrix2, rather
>> than the newer version (https://github.com/jdtournier/mrtrix3), so it's
>> worth pointing that out too. Some extra detail would make it easier for the
>> experts to point you in the right direction. Good luck!
>>
>> Kind regards,
>> Ivan Alvarez
>>
>> PhD Candidate
>> Imaging and Biophysics Unit
>> UCL Institute of Child Health
>> 30 Guilford Street, London, WC1N 1EH
>>
>> On 24/03/2015 09:17, Matthieu Vanhoutte wrote:
>>
>>    Dear MRtrix's experts,
>>
>>  I am trying to compute tracts of the facial nerve (nerve VII). In order
>> to succeed in this, I have tried different methods but the results aren't
>> still convincing :
>>
>>  1) I tried to compute tracts from one coordinate seed with radius of 3
>> mm at the entry area of the facial nerve at the brain-stem
>>
>>  OR
>>
>>  2) I tried to compute tracts from one ROI including the visible facial
>> nerve from T1 image
>>
>>  Could you propose me any other method I should try ?
>>
>>  Best regards,
>>
>>      -------------------------------------
>> Matthieu Vanhoutte, MSc
>>  Research Engineer - Department of Neuroradiology
>> Regional University Hospital, Lille, France
>>
>>
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-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*

*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
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