[Mrtrix-discussion] Difficulty in estimating ODFs using CSD on the NKI_enhanced sample

[Donald Tournier]

Hi Ahmad,

I notice your bvals file contains a single b=0 volume with an actual
b-value of 5. MRtrix is currently only able to handle single-shell HARDI
data, and blindly assumes that any non-zero b-value corresponds to one of
the DW images (not ideal, I admit). I suspect all you need to do is set
that first value in your bvals file to an actual zero...

Hope that helps.
Cheers,

Donald.



On 12 July 2013 22:08, A.S. KANAAN <amadeus.kanaan at gmail.com> wrote:

> Hi Dr. Touriner,
>
> I am currently running a Diffusion analysis on the NKI_enhanced<https://www.dropbox.com/home/NKI_enhanced>DWI sample using CSD for estimating the fODFs.
> This is the data acquisition protocol:
> http://fcon_1000.projects.nitrc.org/indi/pro/eNKI_RS_TRT/DIff_137.pdf .
>
> In my process, I have used different maximum harmonic degrees (lmax
> 6,8,14) for estimating the response function and running CSD. The profile
> of the estimate response function looked normal in all three cases and in
> three different subjects (Example<https://docs.google.com/file/d/0B836ny4-YXrTR2lMWEREazFGbTA/edit?usp=sharing>),
> but the fODF estimates were problematic. In all three subjects (ages:
> 46,36,21) several voxels on only one side of the Corpus Collosum contained weird
> fODFs representing crossing fibers.<https://docs.google.com/file/d/0B836ny4-YXrTUUludXhsVzU1S00/edit?usp=sharing>As evident from the glyphs, tractography using both the deterministic and
> probabilistic algorithms (SD_STREAM<https://docs.google.com/file/d/0B836ny4-YXrTTEFablowQjRKQkk/edit?usp=sharing>and
> SD_PROB<https://docs.google.com/file/d/0B836ny4-YXrTUkVyM1NsOG9Sbk0/edit?usp=sharing>)
> did not generate anatomically sounds tracts. I tried using different radii
> of curvature and step lengths but the results were similar.
>
> Here is my process...
>
> Masks: A single fiber voxel mask (SF_mask.mif) and a White matter mask
> (WM_mask.mif) were generated from the FA map at thresholds of 0.7 and 0.2
> respectively.
> ERF:  >> estimate_response -grad grad.txt -lmax 8 DWI_ED.nii SF_mask.mif
> ERF_lmax8.txt
> CSD: >> csdeconv -grad grad.txt -mask WM_mask.mif -seed WM_mask.mif -lmax
> 8 DWI_ed.nii ERF_lmax8.txt CSD_lmax8.mif
>
> Looking at the RAW data, we noticed motion artifacts, some noise and
> straight lines that cross the brain on coronal sections (see link below).
>
> Have you encountered this sort of a problem before for an acquisition with
> more than 100 diffusion encoding gradient directions? Is my process sound
> or do you think its a problem with the RAW data?
>
> You can download the raw data as well as my results here<https://www.dropbox.com/sh/xbh77szqmlmrkoj/pAPjPDXcnd>.
>
>
> Viele Grüße,
> Ahmad Kanaan
> __________________________________________________
> Max-Planck-Institut für Kognitions- und Neurowissenschaften
> Stephanstrasse 1a
> 04103 Leipzig, Germany
>
>
>
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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
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