[Mrtrix-discussion] FA and ADC values for a tract

Wed Mar 26 16:32:47 PDT 2014

Hi David.

> Luis, I'm guessing when you say tract-specific, you are averaging the AFD
> within a tract-of-interest? Since AFD is proportional to the intra-axonal
> volume, ideally you need to be summing the AFD to account for differences
> in fibre bundle *width* (as the modulation does in voxel-wise analysis).
>
This is where I still have questions and value your input. What I want in
the end is a volume in which each voxel has the AFD for a specific bundle.
That is, I could have as many of these AFD volumes as dissected bundles.
Let's imagine just one. If I end up with such an AFD volume, I imagine I
could then simply average all the voxels that contain the bundle and get a
tract measurement. I could also sample these AFDs along the tracks and get
a spatially varying AFD.

My question has to do with the summing of AFDs. Do you mean that if 50
streamlines traverse a given voxel, then the AFD for that voxel should be
the sum of 50 AFDs? In theory, these 50 FOD lobes should be very similar
(give or take some interpolation). I still do not understand why summing 50
AFDs would be better than the mean of them. Perhaps I did not understand
correctly, and perhaps I have not expressed myself properly in the sense
that I would like a voxel-wise AFD for a given tract.

Helen: Once I figure out these details, I will be happy to post my script.

>
>
> The next major release of MRtrix will contain SIFT and some AFD tools.
> However, FOD registration probably won't be included until a few months
> after the initial release.
>
Music to my ears!

Luis

>
> On 27 March 2014 08:06, Luis Concha <lconcha at unam.mx> wrote:
>
>> Hi Dorian and fellow mrtrixers.
>>
>> Yes, it is very much like HMOA, which is actuallly just like AFD (*,**) .
>> There is, however, one difference: In the approach I mentioned, the tracts
>> are first computed using the tractography algorithms supplied by
>> streamtrack, and in the paper by Dell'Acqua, HMOA is used to drive the
>> tractography algorithm itself, as well as to select tract-specific HMOA a
>> posteriori (Figure 9 in Dell'Acqua).
>>
>> My main concern is that I use find_SH_peaks in order to simplify the
>> identification of the corresponding (parallel) FOD peak to the tract
>> segment. Given that find_SH_peaks output can be affected by the number of
>> directions used as seeds for  peak finding, is there any min number that
>> should be used? (I used 120).
>>
>>
>> I would be happy to share my scripts to obtain AFD/HMOA, if anyone is
>> interested.
>>
>>
>> (*) Marco Catani, during the ISMRM Diffusion Workshop last year, said
>> that it was one of the rewiewers who asked them to change AFD to HMOA.
>> (**) One key point in Raffelt's paper on AFD is the implementation of a
>> voxel-based framework for the analysis of this measurement for group
>> analyses, which I am hoping will be available in mrtrix soon.
>>
>> Luis
>>
>>
>>
>>
>>
>> On Wed, Mar 26, 2014 at 2:17 PM, Dorian P. <alb.net at gmail.com> wrote:
>>
>>> Hello everybody, hello Dr. Concha.
>>>
>>> As we are on the topic, it seems to me the idea of Dr. Concha is similar
>>> to the HMOA measure of Dell'Acqua et al.
>>> http://www.ncbi.nlm.nih.gov/pubmed/22488973
>>>
>>> Am I correct thinking they are similar, if not identical measures?
>>>
>>> I am looking for ways to obtain this measure in mrtrix. Anyone can give
>>> some hints or share the steps to do this? Will mrtrix plan to output the
>>> amplitude of FODs for tracts in next releases?
>>>
>>>
>>> Thank you
>>> Dorian
>>> Thomas Jefferson University
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Mar 26, 2014 at 3:58 PM, Luis Concha <lconcha at unam.mx> wrote:
>>>
>>>>
>>>> Hi Thijs.
>>>>
>>>> It is great to know that the new release of mrtrix will have tools for
>>>> AFD. In the meantime, I have played around with some scripts to obtain such
>>>> a measurement in a tract-specific way and I would appreciate your input and
>>>> that of others in this list. The scripts do this:
>>>>
>>>> 1. Perform tractography and select a set of streamlines for analysis.
>>>> 2. For each streamline segment (i.e., the straight line between two
>>>> adjacent steps), find the FOD lobe that is most parallel (dot product
>>>> between streamline segment and FOD peaks).
>>>> 3. Once the FOD lobe has been identified, extract its amplitude
>>>> (tract-specific AFD).
>>>>
>>>> I am assuming that if DWI signal is normalized (as you mentioned), then
>>>> FOD amplitudes should be comparable between subjects. Also, since there is
>>>> no spatial normalization of images, there is no need to modulate the AFD to
>>>> compensate for the spatial transformation.
>>>>
>>>> If you find any flaws with this, please let me know. Oh, and if you
>>>> could give us a teaser of what new features we will see in the new release
>>>> of mrtrix, that would be fantastic!
>>>>
>>>>
>>>>
>>>>
>>>> Dr. Luis Concha
>>>> Instituto de Neurobiología
>>>> Laboratorio C-13
>>>> UNAM, Campus Juriquilla
>>>> Boulervard Juriquilla 3001
>>>> Juriquilla, Querétaro.
>>>> C.P. 76230
>>>> México
>>>> Tel (442) 2 38 10 54
>>>> Fax (442) 2 38 10 46
>>>> http://personal.inb.unam.mx/lconcha/
>>>>
>>>>
>>>> On Wed, Mar 26, 2014 at 1:47 PM, Thijs Dhollander <
>>>> thijs.dhollander at gmail.com> wrote:
>>>>
>>>>> Hi Helen,
>>>>>
>>>>> Opinions on FA/ADC quantification can be wildly varying... :-)
>>>>> There's no problem calculating and reporting their values, but
>>>>> interpretation is a big issue: they can be quite sensitive in many cases,
>>>>> but they are always far from specific.  To avoid starting a long rant on
>>>>> how we should abandon these measures as quickly as possible, I'd rather
>>>>> refer to this nice article:
>>>>> http://www.sciencedirect.com/science/article/pii/S1053811912007306 ;
>>>>> it contains some nice and clear passages explaining some of the relevant
>>>>> issues to be wary of, as well as further references that are worth a good
>>>>> read.
>>>>> So the question remains: what's better then?  There's quite some
>>>>> alternatives, but I personally particularly like apparent fibre density
>>>>> (AFD).  A nice and in-depth article on it can be found here:
>>>>> http://www.sciencedirect.com/science/article/pii/S1053811911012092 .
>>>>> Last year's ISMRM had an abstract on some further improvements on analysing
>>>>> AFD:
>>>>> http://cds.ismrm.org/protected/13MPresentations/abstracts/0841.pdf(if you or anyone in your lab attended, they can access it;  the
>>>>> accompanying oral presentation can be found at
>>>>> http://cds.ismrm.org/protected/13MPresentations/0841/ ).  The next
>>>>> big version of MRtrix (expected to be released somewhere around this year's
>>>>> ISMRM in May... ;-)) will contain much more tools that provide you with the
>>>>> means to perform such analyses.
>>>>> In the mean time, you can already easily obtain an (orientationally
>>>>> averaged) AFD map by simply calculating the average of your (normalized)
>>>>> DWI images from a single shell acquisition.  The same contrast (up to a
>>>>> fixed constant factor) can also be obtained by opening up the result from
>>>>> an SH fit of the signal (or even a CSD outcome) in mrview, and looking at
>>>>> the first coefficient (i.e. the 0th order).
>>>>>
>>>>> Hope this already helps somewhat!
>>>>>
>>>>> Cheers,
>>>>> Thijs
>>>>>
>>>>> PS: now that I've mentioned the upcoming ISMRM; I'd like to encourage
>>>>> everyone on this list that still has many questions (or not) to surely
>>>>> attend and look for each other -- discussions on these new and better ways
>>>>> of quantifying are always much more lively in person :-)
>>>>>
>>>>>
>>>>>
>>>>> *Thijs Dhollanderthijs.dhollander at gmail.com
>>>>> <thijs.dhollander at gmail.com> Tel. +32 475 36 44 27
>>>>> <%2B32%20475%2036%2044%2027>*
>>>>> Medical Image Computing (MIC), ESAT-PSI, Department of Electrical
>>>>> Engineering, KU Leuven
>>>>>
>>>>>
>>>>> On Wed, Mar 26, 2014 at 4:52 PM, Helen Carlson <
>>>>> Helen.Carlson at albertahealthservices.ca> wrote:
>>>>>
>>>>>> Hello Thijs
>>>>>>
>>>>>> Thank-you for your reply to my question. I would like to quantify
>>>>>> changes in white matter over time, specifically pre/post treatment. Is
>>>>>> there a better way to do this than using the mean FA and ADC? Or is this
>>>>>> measurement appropriate?
>>>>>>
>>>>>> Thanks again
>>>>>>
>>>>>> Helen.
>>>>>>
>>>>>>
>>>>>>
>>>>>> *From:* mrtrix-discussion-bounces at www.nitrc.org [mailto:
>>>>>> mrtrix-discussion-bounces at www.nitrc.org] *On Behalf Of *Thijs
>>>>>> Dhollander
>>>>>> *Sent:* March 23, 2014 9:47
>>>>>> *To:* mrtrix-discussion at www.nitrc.org
>>>>>> *Subject:* Re: [Mrtrix-discussion] FA and ADC values for a tract
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hi Helen,
>>>>>>
>>>>>> What you're seeing is (probably) correct: FAs larger than 1 and ADCs
>>>>>> below 0 can appear due to the tensor estimation in MRtrix being a simple
>>>>>> (unconstrained) linear least squares one.  The tensors are not explicitely
>>>>>> constrained to be positive definite, and thus negative eigenvalues might
>>>>>> appear.  When one or more eigenvalues of a given tensor are negative, the
>>>>>> FA can go beyond 1, while the ADC can go below 0.
>>>>>>
>>>>>> Cheers,
>>>>>> Thijs
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> *Thijs Dhollander thijs.dhollander at gmail.com
>>>>>> <thijs.dhollander at gmail.com>Tel. +32 475 36 44 27
>>>>>> <%2B32%20475%2036%2044%2027>*
>>>>>> Medical Image Computing (MIC), ESAT-PSI, Department of Electrical
>>>>>> Engineering, KU Leuven
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Mar 21, 2014 at 10:10 PM, Helen Carlson <
>>>>>> Helen.Carlson at albertahealthservices.ca> wrote:
>>>>>>
>>>>>> Hello all,
>>>>>>
>>>>>> I would like to determine the average FA and ADC values for a given
>>>>>> track (in this case, the arcuate). So I followed previous directions posted
>>>>>> here and have used the following commands on my arcuate which successfully
>>>>>> creates a probability mask for FA and ADC:
>>>>>>
>>>>>>
>>>>>>
>>>>>> tracks2prob -template fa.mif Arcuate.tck FA_mask.mif
>>>>>>
>>>>>> tracks2prob -template adc.mif Arcuate.tck ADC_mask.mif
>>>>>>
>>>>>>
>>>>>>
>>>>>> I then used mrstats to get the average, max, min etc of the tracks by
>>>>>> using these commands:
>>>>>>
>>>>>>
>>>>>>
>>>>>> mrstats fa.mif -mask FA_mask.mif
>>>>>>
>>>>>> mrstats adc.mif -mask ADC_mask.mif
>>>>>>
>>>>>>
>>>>>>
>>>>>> Which also seemed to work except that I was expecting my FA to range
>>>>>> from 0.1 to 1.0 (approximately). Instead, the FA values have a min of 0 and
>>>>>> a max of 1.13. In addition, my ADC values have a negative minimum
>>>>>> (-0.0024). It seems these values are out of range and do not make sense but
>>>>>> I do not know what I am doing wrong.
>>>>>>
>>>>>>
>>>>>>
>>>>>> Thanks in advance for any help
>>>>>>
>>>>>> Helen
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> *Helen Carlson, Ph.D*
>>>>>>
>>>>>> Neuroimaging Research Associate
>>>>>>
>>>>>> Calgary Pediatric Stroke Program & Neuropsychology
>>>>>>
>>>>>> Alberta Children's Hospital
>>>>>>
>>>>>>
>>>>>> ------------------------------
>>>>>>
>>>>>> This message and any attached documents are only for the use of the
>>>>>> intended recipient(s), are confidential and may contain privileged
>>>>>> information. Any unauthorized review, use, retransmission, or other
>>>>>> disclosure is strictly prohibited. If you have received this message in
>>>>>> error, please notify the sender immediately, and then delete the original
>>>>>> message. Thank you.
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Mrtrix-discussion mailing list
>>>>>> Mrtrix-discussion at www.nitrc.org
>>>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Mrtrix-discussion mailing list
>>>>>> Mrtrix-discussion at www.nitrc.org
>>>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Mrtrix-discussion mailing list
>>>>> Mrtrix-discussion at www.nitrc.org
>>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Mrtrix-discussion mailing list
>>>> Mrtrix-discussion at www.nitrc.org
>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Mrtrix-discussion mailing list
>>> Mrtrix-discussion at www.nitrc.org
>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>
>>>
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>>
>
>
> --
> *David Raffelt (PhD)*
> Postdoctoral Fellow
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7024
> www.florey.edu.au
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20140326/13c7b490/attachment-0001.html>