[Mrtrix-discussion] Urgent global tractography

Thu Mar 27 06:59:51 PDT 2014

Hi Vinay,

Something has clearly gone wrong with the DICOM conversion - you ended up
with an image 768 voxels wide along the x-axis. Can I ask where these data
come from? If you can send me the original DICOM data (using dropbox or
whatever service you think is appropriate), I might be able to figure out
what went wrong and fix the code to handle it (assuming this is a bug in
MRtrix and not an issue with your data themselves). Otherwise, you could
probably use the dcm2nii tool, although I have no experience with it, and
you'd then need to convert your DW information into MRtrix format (others
on this list should be able to help with that).

Cheers,
Donald.

On 27 March 2014 11:30, Vinay Kumar Shukla <vinaykumar.shukla at univr.it>wrote:

> Hello Everyone!!
>
> I converted dicom data using mrconvert.
> vips at Sebastian:~/Scrivania/data/Stroke/Control_001/tp1/1__RAWDATA$ mrinfo
> dwi.mif
> ************************************************
> Image:               "dwi.mif"
> ************************************************
>   Format:            MRtrix
>   Dimensions:        768 x 96 x 34
>   Voxel size:        2.20833 x 2.20833 x 3
>   Dimension labels:  0. left->right (mm)
>                      1. posterior->anterior (mm)
>                      2. inferior->superior (mm)
>   Data type:         32 bit float (little endian)
>   Data layout:       [ -0 +1 +2 ]
>   Data scaling:      offset = 0, multiplier = 1
>   Comments:          3T 2D EP TR=6000ms/TE=136ms/FA=90deg 20-Jan-2009
> 13:8:25.938 Mosaic
>   Transform:                    1           0           0      -103.8
>                                -0           1           0      -81.99
>                                -0           0           1       -38.2
>                                 0           0           0           1
>
> but when I used dwi2tensor it says
>
> vips at Sebastian:~/Scrivania/data/Stroke/Control_001/tp1/1__RAWDATA$
> dwi2tensor dwi.mif dt.mif
> dwi2tensor: dwi image should contain at least 4 dimensions
>
> Can any body help me out what went wrong.
>
> looking forward for reply
>
> kind regards
> vinay
>
> ----- Messaggio originale -----
> Da: "Thijs Dhollander" <thijs.dhollander at gmail.com>
> A: "MRtrix discussion" <mrtrix-discussion at www.nitrc.org>
> Inviato: Mercoledì, 26 marzo 2014 17:46:05
> Oggetto: Re: [Mrtrix-discussion] Urgent global tractography
>
>
>
>
>
> Hi Vinay,
>
> I'm not 100% sure, but I suppose you might have been confusing the term
> "global tractography" with "whole-brain tractography"; is that correct?
>
> If so, a good step-by-step tutorial on doing (whole-brain) tractography
> using MRtrix is provided in the manual:
> http://www.brain.org.au/software/mrtrix/tractography/index.html
>
>
>
>
> An detailed overview on the parameters/choices offered by MRtrix, and
> their impact on the final result is provided in the following paper:
> http://onlinelibrary.wiley.com/doi/10.1002/ima.22005/full
>
>
> Hope this helps! :-)
>
>
> Cheers,
> Thijs
>
>
>
> Thijs Dhollander
> thijs.dhollander at gmail.com
> Tel. +32 475 36 44 27
> Medical Image Computing (MIC), ESAT-PSI, Department of Electrical
> Engineering, KU Leuven
>
>
> On Wed, Mar 26, 2014 at 5:05 PM, Vinay Kumar Shukla <
> vinaykumar.shukla at univr.it > wrote:
>
>
> Dear Daan,
> thanks for your kind reply and update.
> I mean steps need to follow to do tractography
> using Mrtrix. Because I look at documentaion
> and bit confuse from to start. I have DW data sets and grad file in text.
> What should I do and how to process it using mrtirx.
> any help would be really grateful.
> kind regards
> vinay
>
> ----- Messaggio originale -----
> Da: "Daan Christiaens" < Daan.Christiaens at esat.kuleuven.be >
> A: "Vinay Kumar Shukla" < vinaykumar.shukla at univr.it >,
> mrtrix-discussion at www.nitrc.org
> Inviato: Mercoledì, 26 marzo 2014 16:58:12
> Oggetto: Re: [Mrtrix-discussion] Urgent global tractography
>
> Dear Vinay,
>
> MRtrix does not offer global tractography for the moment. I¹m developing
> an add-on for this, but it¹s not yet ready to share. In the mean time,
> check out MITK Diffusion ( http://www.mitk.org/DiffusionImaging ).
>
> Best regards,
>
> Daan
>
>
> ir. Daan Christiaens
> Ph.D. Researcher
>
> <mailto: daan.christiaens at uzleuven.be > daan.christiaens at esat.kuleuven.be
> tel +32 16 34 90 35
> fax +32 16 34 90 01
>
> Medical Image Computing  ESAT/PSI  Department of Electrical Engineering
>
> Medical Imaging Research Center < http://www.medicalimagingcenter.be/ > |
> Katholieke Universiteit Leuven < http://www.kuleuven.be/ > | campus
> Gasthuisberg < http://www.uzleuven.be/ > | Herestraat 49 bus 7003 | B -
> 3000
> Leuven
>
>
>
>
>
> On 26/03/14 16:40, "Vinay Kumar Shukla" < vinaykumar.shukla at univr.it >
> wrote:
>
> >Hello Everyone!
> >
> >I want to use mrtrix for global tractography.
> >It is possible can any one help me out what would be the
> >step by step process need to follow with DW data sets.
> >looking forward for reply & kind help
> >many thanks in advance
> >cheers !!
> >vinay
> >
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-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*

*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
*T: +44 (0)20 7188 7118 ext 53613*
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