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

David Raffelt d.raffelt at brain.org.au
Wed Apr 2 23:35:22 PDT 2014 

Hi Luis,
Apologies for the slow reply. The upcoming release of MRtrix has a command
to do exactly what you are after (currently called afdconnectivity).
However, instead of computing the AFD using the peak amplitude for each
fibre population, it computes the integral of the 'lobe'.

On a related note, to make our life easier we have coined a new term
'fixel' to refer to a specific *fi*bre population within a single vo*xel*.
This helps to reduce any ambiguity when referring to a quantitative measure
associated with fibre
population/fascicle<http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0048232&representation=PDF>(since
a 'fibre population' or 'fascicle' quantitative measure could easily
be misinterpreted being related to the *whole* fibre bundle/tract).

With respect to computing a bundle/tract AFD measure, the new
afdconnectivity command uses the streamlines to first identify which fixels
belong to the bundle (irrespective of how many streamlines pass through
each fixel).  It then *sums *the AFD for all fixels in the bundle and then
normalises by the mean streamline length (since the total AFD (intra-axonal
volume) across the width of a bundle is more relevant to connectivity than
bundle length). The afdconnectivity command will also optionally output the
bundle-specific AFD image.

Just to reiterate, afdconnectivity is really a poor mans measure of SIFT-ed
track counts. If you SIFT streamlines using DWIs with proper intensity
normalisation and use the same SIFT proportionality coefficient for all
subjects, then track count can be used as a measure of 'connectivity'.
SIFT-ed track counts should in theory be more bundle specific if your
bundle (at some point along its length) merges with another bundle you are
*not* interested in).

Hope this makes sense!
Cheers,
Dave




On 27 March 2014 10:32, Luis Concha <lconcha at unam.mx> wrote:

> 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
>>
>
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>


-- 
*David Raffelt (PhD)*
Post Doctoral 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/20140403/9cfd428e/attachment-0001.html>

More information about the Mrtrix-discussion mailing list