<div dir="ltr"><div>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).<br>
<br>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).<br><br></div>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.<br>
</div><div class="gmail_extra"><br clear="all"><div><div dir="ltr">Dr. Luis Concha<br>Instituto de Neurobiología<br>Laboratorio C-13<br>UNAM, Campus Juriquilla<br>Boulervard Juriquilla 3001<br>Juriquilla, Querétaro.<br>C.P. 76230<br>
México<br>Tel (442) 2 38 10 54<br>Fax (442) 2 38 10 46<br><a href="http://personal.inb.unam.mx/lconcha/" target="_blank">http://personal.inb.unam.mx/lconcha/</a><br></div></div>
<br><br><div class="gmail_quote">On Thu, Mar 27, 2014 at 10:07 AM, 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">
<br>
Hello!<br>
I will send you the dicom file. But hereis another problem with bvalue<br>
vips@Sebastian:~/Scrivania/data/Stroke/Control_001/tp1/1__RAWDATA/DSI$ sudo mrinfo -grad encoding.b dwi.mif<br>
[sudo] password for vips:<br>
<div class="">************************************************<br>
Image: "dwi.mif"<br>
************************************************<br>
Format: MRtrix<br>
</div> Dimensions: 96 x 96 x 34 x 515<br>
Voxel size: 2.20833 x 2.20833 x 3 x 6<br>
<div class=""> Dimension labels: 0. left->right (mm)<br>
1. posterior->anterior (mm)<br>
2. inferior->superior (mm)<br>
</div> 3. undefined (?)<br>
Data type: signed 16 bit integer (little endian)<br>
Data layout: [ -0 +1 +2 +3 ]<br>
<div class=""> Data scaling: offset = 0, multiplier = 1<br>
</div> Comments: ?TR:6000.000 TE:13<br>
<div class=""> 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>
</div>when I am using this using dw2tensor it says dwi2tensor: unexpected diffusion encoding matrix dimensions....<br>
<br>
Please help me out what went wrong here ????<br>
many thanks<br>
<div class=""><br>
kind regards<br>
vinay<br>
<br>
<br>
----- Messaggio originale -----<br>
</div>Da: "Donald Tournier" <<a href="mailto:jdtournier@gmail.com">jdtournier@gmail.com</a>><br>
<div class="">A: "Vinay Kumar Shukla" <<a href="mailto:vinaykumar.shukla@univr.it">vinaykumar.shukla@univr.it</a>><br>
</div>Cc: "Thijs Dhollander" <<a href="mailto:thijs.dhollander@gmail.com">thijs.dhollander@gmail.com</a>>, "mrtrix mailinglist" <<a href="mailto:mrtrix-discussion@www.nitrc.org">mrtrix-discussion@www.nitrc.org</a>><br>
Inviato: Giovedì, 27 marzo 2014 14:59:51<br>
<div><div class="h5">Oggetto: Re: [Mrtrix-discussion] Urgent global tractography<br>
<br>
<br>
<br>
Hi Vinay,<br>
<br>
<br>
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).<br>
<br>
<br>
Cheers,<br>
Donald.<br>
<br>
<br>
<br>
<br>
<br>
On 27 March 2014 11:30, Vinay Kumar Shukla < <a href="mailto:vinaykumar.shukla@univr.it">vinaykumar.shukla@univr.it</a> > wrote:<br>
<br>
<br>
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>
<br>
<br>
kind regards<br>
vinay<br>
<br>
----- Messaggio originale -----<br>
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>
<br>
<br>
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. <a href="tel:%2B32%20475%2036%2044%2027" value="+32475364427">+32 475 36 44 27</a><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 <a href="tel:%2B32%2016%2034%2090%2035" value="+3216349035">+32 16 34 90 35</a><br>
fax <a href="tel:%2B32%2016%2034%2090%2001" value="+3216349001">+32 16 34 90 01</a><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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--<br>
<br>
Dr J-Donald Tournier (PhD)<br>
<br>
<br>
Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London<br>
<br>
<br>
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