<div dir="ltr"><div>Hi Vinay,</div><div><br></div><div>Something has clearly gone wrong with the DICOM conversion - you ended up with an image <span style="font-family:arial,sans-serif;font-size:13px">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). </span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">Cheers,</span></div><div><span style="font-family:arial,sans-serif;font-size:13px">Donald.</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 27 March 2014 11:30, Vinay Kumar Shukla <span dir="ltr"><<a href="mailto:vinaykumar.shukla@univr.it" target="_blank">vinaykumar.shukla@univr.it</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello Everyone!!<br>
<br>
I converted dicom data using mrconvert.<br>
vips@Sebastian:~/Scrivania/data/Stroke/Control_001/tp1/1__RAWDATA$ mrinfo dwi.mif<br>
************************************************<br>
Image: "dwi.mif"<br>
************************************************<br>
Format: MRtrix<br>
Dimensions: 768 x 96 x 34<br>
Voxel size: 2.20833 x 2.20833 x 3<br>
Dimension labels: 0. left->right (mm)<br>
1. posterior->anterior (mm)<br>
2. inferior->superior (mm)<br>
Data type: 32 bit float (little endian)<br>
Data layout: [ -0 +1 +2 ]<br>
Data scaling: offset = 0, multiplier = 1<br>
Comments: 3T 2D EP TR=6000ms/TE=136ms/FA=90deg 20-Jan-2009 13:8:25.938 Mosaic<br>
Transform: 1 0 0 -103.8<br>
-0 1 0 -81.99<br>
-0 0 1 -38.2<br>
0 0 0 1<br>
<br>
but when I used dwi2tensor it says<br>
<br>
vips@Sebastian:~/Scrivania/data/Stroke/Control_001/tp1/1__RAWDATA$ dwi2tensor dwi.mif dt.mif<br>
dwi2tensor: dwi image should contain at least 4 dimensions<br>
<br>
Can any body help me out what went wrong.<br>
<br>
looking forward for reply<br>
<div class=""><br>
kind regards<br>
vinay<br>
<br>
----- Messaggio originale -----<br>
</div>Da: "Thijs Dhollander" <<a href="mailto:thijs.dhollander@gmail.com">thijs.dhollander@gmail.com</a>><br>
A: "MRtrix discussion" <<a href="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</a>><br>
Inviato: Mercoledì, 26 marzo 2014 17:46:05<br>
<div class="HOEnZb"><div class="h5">Oggetto: Re: [Mrtrix-discussion] Urgent global tractography<br>
<br>
<br>
<br>
<br>
<br>
Hi Vinay,<br>
<br>
I'm not 100% sure, but I suppose you might have been confusing the term "global tractography" with "whole-brain tractography"; is that correct?<br>
<br>
If so, a good step-by-step tutorial on doing (whole-brain) tractography using MRtrix is provided in the manual: <a href="http://www.brain.org.au/software/mrtrix/tractography/index.html" target="_blank">http://www.brain.org.au/software/mrtrix/tractography/index.html</a><br>
<br>
<br>
<br>
<br>
An detailed overview on the parameters/choices offered by MRtrix, and their impact on the final result is provided in the following paper: <a href="http://onlinelibrary.wiley.com/doi/10.1002/ima.22005/full" target="_blank">http://onlinelibrary.wiley.com/doi/10.1002/ima.22005/full</a><br>
<br>
<br>
Hope this helps! :-)<br>
<br>
<br>
Cheers,<br>
Thijs<br>
<br>
<br>
<br>
Thijs Dhollander<br>
<a href="mailto:thijs.dhollander@gmail.com">thijs.dhollander@gmail.com</a><br>
Tel. +32 475 36 44 27<br>
Medical Image Computing (MIC), ESAT-PSI, Department of Electrical Engineering, KU Leuven<br>
<br>
<br>
On Wed, Mar 26, 2014 at 5:05 PM, Vinay Kumar Shukla < <a href="mailto:vinaykumar.shukla@univr.it">vinaykumar.shukla@univr.it</a> > wrote:<br>
<br>
<br>
Dear Daan,<br>
thanks for your kind reply and update.<br>
I mean steps need to follow to do tractography<br>
using Mrtrix. Because I look at documentaion<br>
and bit confuse from to start. I have DW data sets and grad file in text.<br>
What should I do and how to process it using mrtirx.<br>
any help would be really grateful.<br>
kind regards<br>
vinay<br>
<br>
----- Messaggio originale -----<br>
Da: "Daan Christiaens" < <a href="mailto:Daan.Christiaens@esat.kuleuven.be">Daan.Christiaens@esat.kuleuven.be</a> ><br>
A: "Vinay Kumar Shukla" < <a href="mailto:vinaykumar.shukla@univr.it">vinaykumar.shukla@univr.it</a> >, <a href="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</a><br>
Inviato: Mercoledì, 26 marzo 2014 16:58:12<br>
Oggetto: Re: [Mrtrix-discussion] Urgent global tractography<br>
<br>
Dear Vinay,<br>
<br>
MRtrix does not offer global tractography for the moment. I¹m developing<br>
an add-on for this, but it¹s not yet ready to share. In the mean time,<br>
check out MITK Diffusion ( <a href="http://www.mitk.org/DiffusionImaging" target="_blank">http://www.mitk.org/DiffusionImaging</a> ).<br>
<br>
Best regards,<br>
<br>
Daan<br>
<br>
<br>
ir. Daan Christiaens<br>
Ph.D. Researcher<br>
<br>
<mailto: <a href="mailto:daan.christiaens@uzleuven.be">daan.christiaens@uzleuven.be</a> > <a href="mailto:daan.christiaens@esat.kuleuven.be">daan.christiaens@esat.kuleuven.be</a><br>
tel +32 16 34 90 35<br>
fax +32 16 34 90 01<br>
<br>
Medical Image Computing ESAT/PSI Department of Electrical Engineering<br>
<br>
Medical Imaging Research Center < <a href="http://www.medicalimagingcenter.be/" target="_blank">http://www.medicalimagingcenter.be/</a> > |<br>
Katholieke Universiteit Leuven < <a href="http://www.kuleuven.be/" target="_blank">http://www.kuleuven.be/</a> > | campus<br>
Gasthuisberg < <a href="http://www.uzleuven.be/" target="_blank">http://www.uzleuven.be/</a> > | Herestraat 49 bus 7003 | B - 3000<br>
Leuven<br>
<br>
<br>
<br>
<br>
<br>
On 26/03/14 16:40, "Vinay Kumar Shukla" < <a href="mailto:vinaykumar.shukla@univr.it">vinaykumar.shukla@univr.it</a> > wrote:<br>
<br>
>Hello Everyone!<br>
><br>
>I want to use mrtrix for global tractography.<br>
>It is possible can any one help me out what would be the<br>
>step by step process need to follow with DW data sets.<br>
>looking forward for reply & kind help<br>
>many thanks in advance<br>
>cheers !!<br>
>vinay<br>
><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br></font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div>
<i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br>
</font></i></div><div><i><font color="#990000"><b>T:</b> +44 (0)20 7188 7118 ext 53613</font></i></div></div><div><i><font color="#990000"><b>W:</b> <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i><br>
</div></div>
</div>