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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">The nifti file contains only 3 dimensions:
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<div>>mrinfo 20120423_192519ep2ddiffs005a1001.nii.gz</div>
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<div>Image: "20120423_192519ep2ddiffs005a1001.nii.gz"</div>
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<div> Format: NIfTI-1.1</div>
<div> Dimensions: 96 x 48 x 65</div>
<div> Voxel size: 2.5 x 2.5 x 10</div>
<div> Dimension labels: 0. left->right (mm)</div>
<div> 1. posterior->anterior (mm)</div>
<div> 2. inferior->superior (mm)</div>
<div> Data type: signed 16 bit integer (little endian)</div>
<div> Data layout: [ -0 +1 +2 ]</div>
<div> Data scaling: offset = 0, multiplier = 1</div>
<div> Comments: ?TR:2000.000 TE:76</div>
<div> Transform: 0.9992 0 0.04022 -100.3</div>
<div> 0.001893 0.9989 -0.04703 -41.88</div>
<div> -0.04018 0.04707 0.9981 -2.113</div>
<div> 0 0 0 1</div>
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<div>So it's only a single 3D volume, presumably the b=0 image, so something went wrong with the conversion.</div>
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<div>In addition to that you will also need to supply the gradient orientations and b-values if you want to be able to do a DTI fit. </div>
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<div>What you could try is to convert the directory with the ima files with mrtrix, using the mrconvert command. There's a good chance that mrconvert will be able to convert the full 4D data set and associated gradient orientations.</div>
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<div>Cheers,</div>
<div>Ben<br>
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<font size="1">Ben Jeurissen, Ph.D.</font></div>
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<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">Post-doctoral researcher</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">Vision Lab, Dept. of Physics</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">University of Antwerp</font></div>
<div><font size="1">Universiteitsplein 1, N.1.18</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">B-2610 Wilrijk, Belgium</font></div>
<div><font size="1">Phone: +32 3 265 24 77</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">Email: ben.jeurissen@ua.ac.be</font></div>
<div style="font-weight:normal; color:rgb(0,0,0)"><font size="1">Url: <a title="http://visielab.ua.ac.be/people/ben-jeurissen
Ctrl+Click to follow link" href="http://visielab.ua.ac.be/people/ben-jeurissen" target="_blank">http://visielab.ua.ac.be/people/ben-jeurissen</a></font></div>
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<div id="divRpF838180" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> mrtrix-discussion-bounces@public.nitrc.org [mrtrix-discussion-bounces@public.nitrc.org] on behalf of Jesse Ross-Jones [jesse.rj@gmail.com]<br>
<b>Sent:</b> 22 March 2013 10:13<br>
<b>To:</b> mrtrix-discussion@public.nitrc.org<br>
<b>Subject:</b> [Mrtrix-discussion] fiber tractography of a phantom<br>
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I am using the phantom created by DKFZ project available here <a href="http://www.nitrc.org/projects/diffusion-data/" target="_blank">
http://www.nitrc.org/projects/diffusion-data/</a><br>
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In order to be able to read the images in MRtrix I first had to convert the .ima files to nii.gz with the dcm2nii tool available from mricron. At this point I am able to view the volume in mrview, however, when I attempt to compute the tensors, I receive the
following error: <br>
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C:\Program Files (x86)\MRtrix\bin>dwi2tensor C:\temp\phantom_output\20120423_192519ep2ddiffs005a1001.nii.gz C:\temp\phantom_output\dt.mif<br>
<b>dwi2tensor: dwi image should contain at least 4 dimension<br>
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</b>I have attached the nii volume here, is the file incorrectly converted, or does the problem lie elsewhere?<br>
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<div>Many thanks!<br>
Jesse<br>
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