[Mrtrix-discussion] multiple bvalue
romain valabregue
romain.valabregue at upmc.fr
Wed Jul 3 05:49:13 PDT 2013
Dear all
Summer is there (and vacations are coming) so it may not be the perfect
time to put it forward. But just in case ...
Since I am playin with the very nice connectome data I can not stop
thinking : it would be great to have a multi shell version of the odf
within mrtrix.
Have a look at connectome data It may give you the motivation ... 288
direction (with 3 shell 1000 2000 3000) 1.25 isotropic resolution
perfect corregistration with a T1 0.7iso volume, 40 subject easy to
dowload.
It is worth to try !
All the best
Romain
Le 16/11/2012 02:31, Donald Tournier a écrit :
> Hi everyone,
>
> The DTI fit in MRtrix should handle multiple b-values fine. The CSD
> approach however cannot currently handle such data, as Thijs correctly
> stated. Luis, I'm surprised that you manage to get convincing results
> simply by stripping off the b=0 image, since it is ignored by csdeconv
> anyway (unless you use the -normalise option which is not
> recommended). In any case, it is definitely not designed to handle
> multiple b-values, so I would not advise planning your study around it...
>
> Cheers,
>
> Donald.
>
>
> On 16 November 2012 07:41, Luis Concha <lconcha at unam.mx
> <mailto:lconcha at unam.mx>> wrote:
>
> I have a similar data set to the one described by Romain (1x b=0,
> 32x b=1000 and 32x b=2000; the 32 gradient directions are
> identical for b1000 and b2000).
>
> Perhaps I _shouldn't_ be doing it, but cdsdeconv seems to handle
> this data set perfectly when I strip off the b=0 image (my usual
> approach, as I am after CSF signal elimination). However, I just
> tested csdeconv with all three b values (0,1000 and 2000) and it
> seems to give similar results, up to an lmax=6 (I did not test any
> further).
>
> The DTI maps look perfectly fine, with a slight increase in FA in
> regions partial voluming with CSF (fornix, callosum edges) in the
> non-b0 data set as compared to the b=0,1000,2000 data set.
>
> Perhaps doing 2 shells is OK even in the absence of b=0, and the
> argument of multi-shell CSD invalidity is only applicable for >3
> shells. Nonetheless, I would much appreciate it if you could
> direct me to the right papers in order to understand if I am doing
> things properly, as I plan to use this approach for a longitudinal
> 4-year study that is just about to begin.
>
> Below is the gradient table used for the b=0,1000,2000 data set,
> and I am posting a snapshot of the orientation plots for the data
> sets I mentioned here:
> http://imgur.com/56Y8q
>
>
> Thanks.
>
>
> Dr. Luis Concha
> Instituto de Neurobiología
> Laboratorio C-12
> UNAM, Campus Juriquilla
> Boulervard Juriquilla 3001
> Juriquilla, Querétaro.
> C.P. 76230
> México
> Tel (442) 2 38 10 53 <tel:%28442%29%202%2038%2010%2053>
> Fax (442) 2 38 10 46 <tel:%28442%29%202%2038%2010%2046>
> www.inb.unam.mx <http://www.inb.unam.mx>
>
> 0.000000 0.000000 0.000000 0
> -1.000000 0.000000 0.000000 1000
> 0.000000 -1.000000 0.000000 1000
> 0.000000 0.000000 1.000000 1000
> 0.042400 0.114601 -0.992506 1000
> -0.174909 0.200511 -0.963951 1000
> -0.232290 0.162593 -0.958960 1000
> -0.367520 -0.026101 -0.929649 1000
> -0.190192 -0.374383 -0.907560 1000
> 0.116799 -0.833394 -0.540196 1000
> 0.200489 -0.252686 -0.946548 1000
> 0.495782 -0.134495 -0.857969 1000
> 0.014100 0.628102 -0.778003 1000
> 0.744490 0.147698 -0.651091 1000
> 0.760877 -0.320390 -0.564283 1000
> 0.180892 -0.924660 -0.335085 1000
> 0.679628 0.422417 -0.599725 1000
> -0.777100 -0.470700 -0.417800 1000
> -0.924162 0.103596 -0.367685 1000
> -0.468485 0.767376 -0.437786 1000
> -0.881688 0.189298 -0.432194 1000
> -0.690404 -0.706204 -0.156901 1000
> -0.239096 -0.757087 -0.607990 1000
> 0.057800 -0.983696 0.170299 1000
> 0.536773 -0.836058 -0.113494 1000
> 0.991788 0.120698 -0.042299 1000
> 0.996763 -0.070897 -0.037899 1000
> <tel:0.037899%C2%A0%C2%A0%C2%A0%201000>
> 0.872425 -0.478114 -0.101403 1000
> 0.248714 -0.933552 0.258114 1000
> -0.118295 -0.991861 -0.047098 1000
> -0.337598 -0.841495 0.421798 1000
> -0.528585 -0.840876 0.116297 1000
> -0.996853 -0.054997 -0.057097 1000
> -1.000000 0.000000 0.000000 2000
> 0.000000 -1.000000 0.000000 2000
> 0.000000 0.000000 1.000000 2000
> 0.042400 0.114601 -0.992506 2000
> -0.174909 0.200511 -0.963951 2000
> -0.232290 0.162593 -0.958960 2000
> -0.367520 -0.026101 -0.929649 2000
> -0.190192 -0.374383 -0.907560 2000
> 0.116799 -0.833394 -0.540196 2000
> 0.200489 -0.252686 -0.946548 2000
> 0.495782 -0.134495 -0.857969 2000
> 0.014100 0.628102 -0.778003 2000
> 0.744490 0.147698 -0.651091 2000
> 0.760877 -0.320390 -0.564283 2000
> 0.180892 -0.924660 -0.335085 2000
> 0.679628 0.422417 -0.599725 2000
> -0.777100 -0.470700 -0.417800 2000
> -0.924162 0.103596 -0.367685 2000
> -0.468485 0.767376 -0.437786 2000
> -0.881688 0.189298 -0.432194 2000
> -0.690404 -0.706204 -0.156901 2000
> -0.239096 -0.757087 -0.607990 2000
> 0.057800 -0.983696 0.170299 2000
> 0.536773 -0.836058 -0.113494 2000
> 0.991788 0.120698 -0.042299 2000
> 0.996763 -0.070897 -0.037899 2000
> <tel:0.037899%C2%A0%C2%A0%C2%A0%202000>
> 0.872425 -0.478114 -0.101403 2000
> 0.248714 -0.933552 0.258114 2000
> -0.118295 -0.991861 -0.047098 2000
> -0.337598 -0.841495 0.421798 2000
> -0.528585 -0.840876 0.116297 2000
> -0.996853 -0.054997 -0.057097 2000
>
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>
>
>
> --
> *Dr Jacques-Donald Tournier
> *
> Research Fellow
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7033
> Fax: +61 3 9035 7307
> www.florey.edu.au <http://www.florey.edu.au>
>
>
>
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