[Mrtrix-discussion] Urgent global tractography

Vinay Kumar Shukla vinaykumar.shukla at univr.it
Fri Mar 28 00:54:37 PDT 2014 

Hi

Yes I used dcm2nii for conversion and output bval & bvec files are attached.
Please help me out about procedures.
many thanks 
kind regards
vinay

----- Messaggio originale -----
Da: "Luis Concha" <lconcha at unam.mx>
A: "Vinay Kumar Shukla" <vinaykumar.shukla at univr.it>
Cc: "Donald Tournier" <jdtournier at gmail.com>, "MRtrix discussion" <mrtrix-discussion at www.nitrc.org>
Inviato: Giovedì, 27 marzo 2014 17:19:58
Oggetto: Re: [Mrtrix-discussion] Urgent global tractography



This new file shows a correctly organzed data set, with 4 dimensions, as opposed to the previous one, which was 3D. It is surprising how many volumes there are, but this may (or may not) be the case, depending on your acquisition. I imagine these are different files? (by the way, you do not need to be sudo to run mrinfo). 

How many lines are there in your encoding.b file? you can check this with wc -l encoding.b . The value should match the number of volumes (515). 

Have you tried converting your data with dcm2nii, as Donald suggested? It should output bval and bvec files, which are trivial to convert to an encoding.b file. 




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 Thu, Mar 27, 2014 at 10:07 AM, Vinay Kumar Shukla < vinaykumar.shukla at univr.it > wrote: 



Hello! 
I will send you the dicom file. But hereis another problem with bvalue 
vips at Sebastian:~/Scrivania/data/Stroke/Control_001/tp1/1__RAWDATA/DSI$ sudo mrinfo -grad encoding.b dwi.mif 
[sudo] password for vips: 

************************************************ 
Image: "dwi.mif" 
************************************************ 
Format: MRtrix 
Dimensions: 96 x 96 x 34 x 515 
Voxel size: 2.20833 x 2.20833 x 3 x 6 

Dimension labels: 0. left->right (mm) 
1. posterior->anterior (mm) 
2. inferior->superior (mm) 
3. undefined (?) 
Data type: signed 16 bit integer (little endian) 
Data layout: [ -0 +1 +2 +3 ] 

Data scaling: offset = 0, multiplier = 1 
Comments: ?TR:6000.000 TE:13 

Transform: 1 0 0 -103.8 
-0 1 0 -81.99 
-0 0 1 -38.2 
0 0 0 1 

when I am using this using dw2tensor it says dwi2tensor: unexpected diffusion encoding matrix dimensions.... 

Please help me out what went wrong here ???? 
many thanks 


kind regards 
vinay 


----- Messaggio originale ----- 
Da: "Donald Tournier" < jdtournier at gmail.com > 

A: "Vinay Kumar Shukla" < vinaykumar.shukla at univr.it > 
Cc: "Thijs Dhollander" < thijs.dhollander at gmail.com >, "mrtrix mailinglist" < mrtrix-discussion at www.nitrc.org > 
Inviato: Giovedì, 27 marzo 2014 14:59:51 


Oggetto: Re: [Mrtrix-discussion] Urgent global tractography 



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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>Mrtrix-discussion mailing list 
> Mrtrix-discussion at www.nitrc.org 
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-- 

Dr J-Donald Tournier (PhD) 


Senior Lecturer, Biomedical Engineering 
Division of Imaging Sciences & Biomedical Engineering 
King's College London 


A: Department of Perinatal Imaging & Health, 1 st Floor South Wing, St Thomas' Hospital, London. SE1 7EH 


T: +44 (0)20 7188 7118 ext 53613 
W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering 


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