[Mrtrix-discussion] fiber tractography of a phantom

[Jeurissen Ben]

The nifti file contains only 3 dimensions:

>mrinfo 20120423_192519ep2ddiffs005a1001.nii.gz
************************************************
Image:               "20120423_192519ep2ddiffs005a1001.nii.gz"
************************************************
  Format:            NIfTI-1.1
  Dimensions:        96 x 48 x 65
  Voxel size:        2.5 x 2.5 x 10
  Dimension labels:  0. left->right (mm)
                     1. posterior->anterior (mm)
                     2. inferior->superior (mm)
  Data type:         signed 16 bit integer (little endian)
  Data layout:       [ -0 +1 +2 ]
  Data scaling:      offset = 0, multiplier = 1
  Comments:          ?TR:2000.000 TE:76
  Transform:               0.9992           0     0.04022      -100.3
                         0.001893      0.9989    -0.04703      -41.88
                         -0.04018     0.04707      0.9981      -2.113
                                0           0           0           1


So it's only a single 3D volume, presumably the b=0 image, so something went wrong with the conversion.

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.

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.

Cheers,
Ben



Ben Jeurissen, Ph.D.
Post-doctoral researcher
Vision Lab, Dept. of Physics
University of Antwerp
Universiteitsplein 1, N.1.18
B-2610 Wilrijk, Belgium
Phone: +32 3 265 24 77
Email: ben.jeurissen at ua.ac.be
Url: http://visielab.ua.ac.be/people/ben-jeurissen
________________________________
From: mrtrix-discussion-bounces at public.nitrc.org [mrtrix-discussion-bounces at public.nitrc.org] on behalf of Jesse Ross-Jones [jesse.rj at gmail.com]
Sent: 22 March 2013 10:13
To: mrtrix-discussion at public.nitrc.org
Subject: [Mrtrix-discussion] fiber tractography of a phantom



I am using the phantom created by DKFZ project available here http://www.nitrc.org/projects/diffusion-data/

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:

C:\Program Files (x86)\MRtrix\bin>dwi2tensor C:\temp\phantom_output\20120423_192519ep2ddiffs005a1001.nii.gz C:\temp\phantom_output\dt.mif
dwi2tensor: dwi image should contain at least 4 dimension

I have attached the nii volume here, is the file incorrectly converted, or does the problem lie elsewhere?

Many thanks!
Jesse
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