[Mrtrix-discussion] multiple bvalue
Jeurissen Ben
ben.jeurissen at ua.ac.be
Wed Jul 3 23:53:23 PDT 2013
Hi Romain,
We are working on this. We hope to include it in one of the future releases.
For now, you can process the data by just using the outer shell:
1. Extract a single shell using the mrconvert command:
mrconvert -coord 3 idx1,idx2,... dwi.nii dwib03000.nii
Where idx1,idx2,... is a long list of indices of the b=0 and b=3000 images (indices starting from 0)
Extract the corresponding gradients from your gradient text file and save them in a new txt file.
2. Perform CSD and tracking as before with dwib3000.nii and the reduced grad file.
Cheers,
Ben
-
Ben Jeurissen, Ph.D.
Post-doctoral researcher
Vision Lab, Dept. of Physics
University of Antwerp
Universiteitsplein 1, N.1.18
B-2610 Wilrijk, Belgium
Phone: +32 3 265 24 77
Email: ben.jeurissen at ua.ac.be
Url: http://visielab.ua.ac.be/people/ben-jeurissen
Ben Jeurissen, Ph.D.
Post-doctoral researcher
Vision Lab, Dept. of Physics
University of Antwerp
Universiteitsplein 1, N.1.18
B-2610 Wilrijk, Belgium
Phone: +32 3 265 24 77
Email: ben.jeurissen at ua.ac.be
Url: http://visielab.ua.ac.be/people/ben-jeurissen
________________________________
From: mrtrix-discussion-bounces at public.nitrc.org [mrtrix-discussion-bounces at public.nitrc.org] on behalf of romain valabregue [romain.valabregue at upmc.fr]
Sent: 03 July 2013 14:49
To: mrtrix-discussion at public.nitrc.org
Subject: Re: [Mrtrix-discussion] multiple bvalue
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
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